Mobile supplementation, extraction, and analysis of health records

ABSTRACT

A system, method, and mobile device application are configured to capture, with a mobile device, a document such as a next generation sequencing (NGS) report that includes NGS medical information about a genetically sequenced patient. The method includes receiving, from a mobile device, an image of a medical document comprising NGS medical information of the patient, extracting a first region from the image, extracting NGS medical information of the patient from the first region into a structured dataset, the extracted NGS medical information including at least one RNA expression, correlating a portion of the extracted NGS medical information that includes the at least one RNA expression with summarized medical information from a cohort of patients similar to the patient, and generating, for display on the mobile device, a clinical decision support report comprising the summarized medical information.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/157,974, filed Jan. 25, 2021, which is a continuation of U.S. patentapplication Ser. No. 16/531,005, filed Aug. 2, 2019, and issued as U.S.Pat. No. 10,902,952 on Jan. 26, 2021, which is a continuation of U.S.patent application Ser. No. 16/289,027, filed Feb. 28, 2019, and issuedas U.S. Pat. No. 10,395,772 on Aug. 27, 2019, which claims the benefitof priority to U.S. Provisional Application No. 62/746,997, filed Oct.17, 2018, and to U.S. Provisional Application No. 62/774,854, filed Dec.3, 2018, the contents of each of which are incorporated by referenceherein in their entirety.

BACKGROUND Field of the Invention

A system and method implemented in a mobile platform are describedherein that facilitate the capture of documentation, along with theextraction and analysis of data embedded within the data.

Description of the Related Art

In the medical field, physicians often have a wealth of knowledge andexperience to draw from when making decisions. At the same time,physicians may be limited by the information they have in front of them,and there is a vast amount of knowledge about which the physician maynot be aware or which is not immediately recallable by the physician.For example, many treatments may exist for a particular condition, andsome of those treatments may be experimental and not readily known bythe physician. In the case of cancer treatments, in particular, evenknowing about a certain treatment may not provide the physician with“complete” knowledge, as a single treatment may be effective for somepatients and not for others, even if they have the same type of cancer.Currently, little data or knowledge is available to distinguish betweentreatments or to explain why some patients respond better to certaintreatments than do other patients.

One of the tools from which physicians can draw besides their generalknowledge in order to get a better understanding of a patient'scondition is the patient's electronic health record (“EHR”) orelectronic medical record (“EMR”). Those records, however, may onlyindicate a patient's historical status with respect to a disease, suchas when the patient first presented with symptoms, how it has progressedover time, etc. Current medical records may not provide otherinformation about the patient, such as their genetic sequence, genemutations, variations, expressions, and other genomic information.Conversely, for those patients that have undergone genetic sequencing orother genetic testing, the results of those tests often consist of databut little to no analysis regarding the significance of that data.Without the ability to understand the significance of that report dataand how it relates to their patients' diagnoses, the physicians'abilities to make informed decisions on potential treatment protocolsmay be hindered.

Services exist that can provide context or that can permit detailedanalysis given a patient's genetic information. As discussed, however,those services may be of little use if the physician does not have readyaccess to them. Similarly, even if the physician has access to moredetailed patient information, such as in the form of a lab report from alab provider, and also has access to another company that providesanalytics, the value of that data is diminished if the physician doesnot have a readily available way to connect the two.

Further complicating the process of ensuring that a physician has readyaccess to useful information, with regard to the capture of patientgenetic information through genetic testing, the field of nextgeneration sequencing (“NGS”) for genomics is new. NGS involves usingspecialized equipment such as a next generation gene sequencer, which isan automated instrument that determines the order of nucleotides in DNAand/or RNA. The instrument reports the sequences as a string of letters,called a read. An analyst then compares the read to one or morereference genomes of the same genes, which is like a library of normaland variant gene sequences associated with certain conditions. With nosettled NGS standards, different NGS providers have different approachesfor sequencing patient genomics and, based on their sequencingapproaches, generate different types and quantities of genomics data toshare with physicians, researchers, and patients. Different genomicdatasets exacerbate the task of discerning meaningful genetics-treatmentefficacy insights, as required data may not be in a normalized form, wasnever captured, or simply was never generated.

Another issue that clinicians also experience when attempting to obtainand interpret aspects of EMRs and EHRs is that conventional EHR and EMRsystems lack the ability to capture and store critical components of apatient's history, demographics, diagnosis, treatments, outcomes,genetic markers, etc., because many such systems tend to focus onbilling operations and compliance with regulatory requirements thatmandate collection of a certain subset of attributes. This problem maybe exacerbated by the fact that parts of a patient's record which mayinclude rich and meaningful data (such as diagnoses and treatmentscaptured in progress or follow-up notes, flow sheets, pathology reports,radiology reports, etc.) remain isolated, unstructured, and inaccessiblewithin the patient's record as uncatalogued, unstructured documentsstored in accompanying systems. Conventional methods for identifying andstructuring this data are reliant on human analysts reviewing documentsand entering the data into a record system manually. Many conventionalsystems in use lack the ability to mine and/or uncover this information,leading to gaps in data accessibility and inhibiting a physician'sability to provide optimal care and/or precision medicine.

What is needed are an apparatus, system, and/or method that address oneor more of these challenges.

BRIEF SUMMARY

In one aspect, a method includes the steps of: capturing, with a mobiledevice, a next generation sequencing (NGS) report comprising a NGSmedical information about a sequenced patient; extracting at least aplurality of the NGS medical information using an entity linking engine;and providing the extracted plurality of the NGS medical informationinto a structured data repository.

In another aspect, a method includes the steps of: receiving anelectronic representation of a medical document; matching the documentto a template model; extracting features from the template model usingone or more masks to generate a plurality of expected information types;for each extracted feature, processing the document as a sequence of oneor more masked regions by applying the one or more masks; andidentifying health information from the one or more masked regions, andverifying the identified health information applies to the expectedinformation types.

In yet another aspect, a method includes the steps of capturing an imageof a document using the camera on a mobile device, transmitting thecaptured image to a server, receiving health information abstracted fromthe document from the server, and validating an accuracy of theabstracted health information.

In still another, a system provides mechanisms for automaticallyprocessing clinical documents in bulk, identifying and extracting keycharacteristics, and generating machine learning models that are refinedand optimized through the use of continuous training data.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a depiction of a home screen of a mobile clinician assistantapplication;

FIG. 2 is a depiction of a document capture screen of the application;

FIG. 3 depicts an exemplary tabular extraction approach involving aplurality of different masks;

FIG. 4A is a depiction of a standard report to which the masks of FIG. 3may be applied in order to extract and analyze the data containedtherein;

FIG. 4B is a continuation of the report of FIG. 4A;

FIG. 5 is an exemplary pipeline for processing electronic records intostructured results;

FIG. 6 is an exemplary table representing a structured result;

FIG. 7 is an exemplary constituency-based parse tree representationaccording to an embodiment;

FIG. 8 is an exemplary word weighing representation according to anembodiment;

FIG. 9 is an exemplary sequence labeling classification representationaccording to an embodiment;

FIG. 10 is an exemplary ontological graph database for viewing linksbetween different dictionaries;

FIG. 11 is an exemplary architecture for implementing an embodiment ofthe pipeline of FIG. 5;

FIG. 12 is an exemplary representation of the patient upload portion ofthe architecture;

FIG. 13 is an exemplary representation of the prediction generationportion of the architecture;

FIG. 14 is an exemplary representation of the abstraction portion of thearchitecture;

FIG. 15 is an exemplary representation of the feedback and trainingportion of the architecture;

FIG. 16 is a depiction of a data verification screen of the applicationfor verifying and/or editing data imported into the application and/orpatient record as a result of data capture from one or more documents;

FIG. 17 is a depiction of a first cohort reporting screen of theapplication that includes one or more treatment regimens administered topatients in the cohort, along with relevant response data for eachregimen;

FIG. 18 is a depiction of a second cohort reporting screen that includesthe treatment regimen(s) of FIG. 17, along with relevant adverse eventdata for each regimen;

FIG. 19 is a depiction of a third cohort reporting screen that includespotential clinical trial matches;

FIG. 20 is a flowchart depicting one implementation of the presentdisclosure;

FIG. 21 is a flowchart depicting a second implementation of the presentdisclosure;

FIG. 22 is a flowchart depicting a third implementation of the presentdisclosure;

FIG. 23 is a flowchart depicting a fourth implementation of the presentdisclosure;

FIG. 24 is a flowchart depicting a fifth implementation of the presentdisclosure;

FIG. 25 is a flowchart depicting a sixth implementation of the presentdisclosure;

FIG. 26 is a flowchart depicting a seventh implementation of the presentdisclosure;

FIG. 27 is a flowchart depicting an eighth implementation of the presentdisclosure;

FIG. 28 is a flowchart depicting a ninth implementation of the presentdisclosure; and

FIG. 29 is an exemplary system diagram for carrying out the methodsdescribed herein.

DETAILED DESCRIPTION

With reference to FIG. 1, the present disclosure describes anapplication interface 10 that physicians can reference easily throughtheir mobile or tablet device 12. Through the application interface 10,reports a physician sees may be supplemented with aggregated data (suchas de-identified data from other patients' reports) to provide criticaldecision informing statistics or metrics right to their fingertips.While a mobile or tablet device 12 is referenced herein throughout forthe sake of simplicity and consistency, it will be appreciated that thedevice running the application interface 10 may include any device, suchas a personal computer or other hardware connected through a serverhosting the application, or devices such as mobile cameras that permitthe capturing of digital images for transfer to another hardware systemconnected through a server hosting the application.

An exemplary device may be any device capable of receiving user inputand capturing data a physician may desire to compare against anexemplary cohort to generate treatment recommendations. An exemplarycohort may be a patient cohort, such as a group of patients withsimilarities; those similarities may include diagnoses, responses totreatment regimens, genetic profiles, and/or other medical, geographic,demographic, clinical, molecular, or genetic features.

Generating a report supplement may be performed by a physician byopening or starting-up the application, following prompts provided bythe applications to capture or upload a report or EMR, and validatingany fields from the report that the application automatically populatedfor accuracy. Once captured, the patient's data may be uploaded toserver and analyzed in real time; furthermore, cohort statisticsrelating to the patient's profile may be delivered to the applicationfor the physician's reference and review. The details of thisimplementation, and more, will be discussed with reference to theFigures below.

In one embodiment, as seen in FIG. 1, a home screen 14 of a mobileapplication is displayed on the mobile device 12. The home screen 14 mayprovide access to patient records through a patient interface 18 thatmay provide, for one or more patients, patient identificationinformation 20, such as the patient's name, diagnosis, and recordidentifiers, enabling a user (physician or staff) to identify a patientand to confirm that the record selected by the user and/or presented onthe mobile device 12 relates to the patient that the user wishes toanalyze. In the event that a desired patient is not displayed on thepatient interface 18, the home screen 14 may also include a searchindicator 16 that, upon selection by the user, receives text input suchas a patient's name, unique identifier, or diagnosis, that permits theuser to filter the patients by the search criteria of the text input tosearch for a specific patient. The mobile device 12 may include a touchscreen, through which a user may select a desired patient by touchingthe area on the application interface that includes the desired patientidentification information 20. A cursor (not shown) may appear on thescreen where the user touches to emphasize touch or gestures received.

Alternative home screens may be implemented that provide a user withoptions to perform other functions, as well as to access a patientidentification information screen, and it will be appreciated thatexemplary embodiments referenced herein are not intended to limit theinterface 10 of the application in function or design.

Staying with FIG. 1, a user may add a new patient by selecting acorresponding “add patient” icon 22 on the application or throughgesture recognition. Exemplary gestures may include swiping across thescreen of the mobile device 12 to the left or right, using severalfingers to scroll or swipe, tapping or holding down on a portion of thepatient interface 18 not occupied by patient identification 20, or anyother designated gesture. Alternatively, if no patient data is presentin the patient interface 18, the interface may default to adding a useronce active. Adding a patient may either be performed manually, byentering patient information into the application, or automatically byuploading patient data into the application. Furthermore, automaticuploading may be implemented by capturing an image of patient data atthe mobile device 12, such as from a report, as disclosed below withreference to FIG. 2.

Turning to FIG. 2, once a user has selected a patient, completed addinga new patient, or is adding a new patient from a report, an electronicdocument capture screen 24 may appear. The system may be configured tocapture images of documents that are saved in a plurality of differentformats. Exemplary electronic document captures may include a structureddata form (such as JSON, XML, HTML, etc.), an image (such as JPEG, PNG,etc.), a PDF of a document, report, or file, or a typeface orhandwritten copy of a document, report, or file.

In order to electronically capture a physical copy of a document, theuser may place the document on a surface, such as a surface thatprovides a contrasting color or texture to the document, and aim themobile device's camera at the document so that an image of the documentappears in the document capture screen 24. The user then may select adocument capture icon 26 to begin a document capture process. In analternative embodiment, an automatic capture may be generated oncecapture criteria are met. Exemplary capture criteria may include thatthe document bounds are identifiable and/or that the document is infocus.

During the capture process, or once the document capture icon 26 hasbeen selected, the application 10 may launch a document sensing enginethat applies an algorithm to scan incoming image data from the device'scamera and overlays a document highlight, such as a border or shadedregion 28 on top of the document to visually indicate to the user thebounds of the report currently being captured. The document sensingengine may request that the document be placed on a contrasting surfaceso that the edges of the document, such as the borders of an 8″×10″ or8.5″×11″ sheet of paper, are detectable in the camera frame as well ason the electronic document capture screen 24. Upon detecting a document,the application also may request that the user hold the device 12steady, or still, so a capture may be processed of the document. Afterthe document is captured, the application may prompt the user to takeone of a plurality of additional actions, including, for example,recapturing the image, capturing additional images from the document, orindicating that the user is done with the document capture.

In an alternative embodiment, the application may provide an icon on thecapture screen or the home screen to upload an electronic data capture,image, or digitized file that is already present on the mobile device. Auser may then navigate to the folder on the device containing thedocument and select it for upload. Part of the upload process mayinclude converting the uploaded file into a preferred format for anelectronic data capture.

In one embodiment, an electronic document capture may be generated inblack and white, grayscale, or color. If necessary, the electronicdocument capture may be pre-processed to perform text cleaning and errordetection, such as format conversion, resolution conversion, skewdetection/correction, or batch sizing, resizing, or processing usingdocument processing tools. Once pre-processed, the document may besubmitted for optical character recognition (OCR) on the document toconvert the text into a machine-readable format, such as text, html,JSON, or XML using other document processing tools. Once in amachine-readable format, error correction, such as spell checking, noiseremoval, or context based correlation may be performed on thenow-machine-readable text using still other document processing tools.It should be appreciated that the document processing tools may be asingle tool or may be a collection of tools from which the requisitetool for the processing task is selected in turn. When processingelectronic document captures, many document formats may require formatconversion from an unsupported format to a supported format. Exemplaryconversions may take documents of a variety of formats, including, forexample, XML, HTML, rich text, PDF, PNG, or JPG, and convert them to aformat that a respective OCR service accepts, such as JPG or PNG. Duringformat conversion, additional processing may be performed for parameteroptimization for each respective document to achieve the best resultsfrom the OCR service selected, for example, by converting documents froma source resolution, or dots per inch (dpi), to a resolution bestsupported or by combining multiple requests into one to optimize batchprocessing. Furthermore, another advantage of batch processing isdiscussed below with respect to FIG. 3.

In another embodiment, additional pre-processing may be performed aftersubmitting an image to OCR to determine whether the detected text is“reasonable” before outputting final results. In one example, the word“beast” may rarely occur in an a patient report, for example, as“patient was mauled by unknown beast;” however, “breast” may occur morefrequently, for example, as “patient expresses concern re: lump inbreast,” “breast cancer,” “stage iv breast cancer,” or “patient's breastrecovered from surgery,” giving “breast” a much higher probability ofoccurrence weighting than “beast.” As a result, a reasonabilitydetermination may replace “beast” with “breast,” and indicate that theresulting OCR text is reasonable. While some OCR technologies mayperform their own reasonability determination, it may be necessary tofurther improve upon the quality of the OCR output by performing a textcleaning algorithm on the OCR output.

In one embodiment, a document classifier may process the OCR output ofthe electronic document capture to recognize document identifiers whichare linked to features of the document stored in a predefined model foreach document. Predefined models may also be referred to aspredetermined models. Document identifiers may include Form numbers(such as Form CA217b, Patient Report Rev. 17, AB12937, etc.) indicatinga specific version of a document which provides key health informationin each of the respective document's features. Features of a documentmay include headers, columns, tables, graphs, and other standard formswhich appear in the document.

Exemplary predefined models may be a JSON file, HTML, XML, or otherstructured data. Predefined models may store a list of features that arederived from the document based on MLA processing. The processing mayoccur over a plurality of MLA processing steps and/or sub-steps, each ofwhich may output certain features to the predefined model after eachprocessing step as discussed in further detail below. Each of thesefeatures may additionally have a required or optional tag identifyingwhether the feature must be present or may be present. Furthermore, eachfeature may have a list of expected key health information types. Forexample, a header may expect a patient name, a patient date of birth, aninstitution name, a report date, a diagnosis, etc. The list of featuresand corresponding expected key health information may be encoded intothe predefined model. Furthermore, a mask, natural language processingmodel, and other extraction guidelines may be stored in the predefinedmodel. Extraction guidelines may include reliability checks to ensurethat the information is correct. For example, a diagnosis date may notoccur before birth, or a treatment date may not occur after death.Masks, natural language processing models, and other extractionguidelines are discussed in further detail below and, in addition, withrespect to FIG. 3. Predefined models may be the result of a machinelearning algorithm (MLA) or may be curated by hand for each report type.It should be appreciated that a predefined model may include or excludeadditional criteria and/or differing levels of the above criteria, inaddition to other unmentioned criteria based upon the report type, thecurating method, or user preference.

In another embodiment, document identifiers may be generated from theMLA. A MLA may not generate easily human recognizable patterns, such asthe form numbers above. Instead a MLA may identify a document by pixelarrangements, locations, colors, or other features. For example, astandard report may have a test provider's logo in the top left handcorner of the first page and a header encased in a solid black borderafter the logo. The MLA may identify distinguishing characteristics,pixels, or colors from the logo and the thickness of the border of theheader a seemingly random placement as a unique document identifierwhich is consistent between reports. Furthermore, even if a document isidentified as “Form CA217b”, the MLA may not use the text foridentification purposes but instead identify, for example, that thepixels of the “F” are in a slanted line.

As a result of the OCR output, the application also may identify medicaldata present in the document. Medical data, or key health information,may include numerous fields including, but not limited to, patientdemographics (such as patient name, date of birth, gender, ethnicity,date of death, address, smoking status, diagnosis dates, personalmedical history, or family medical history), clinical diagnoses (such asdate of initial diagnosis, date of metastatic diagnosis, cancer staging,tumor characterization, or tissue of origin), treatments and outcomes(such as therapy groups, medications, surgeries, radiotherapy, imaging,adverse effects, associated outcomes, or corresponding dates), andgenetic testing and laboratory information (such as genetic testing,performance scores, lab tests, pathology results, prognostic indicators,or corresponding dates).

Each of the fields, for example the address, cancer staging,medications, or genetic testing may also have a plurality of subfields.The address field may have subfields for type of use (personal orbusiness), street, city, state, zip, country, and a start or end date(date that residency at the address begins or expires). Genetic testingmay have subfields for the date of genetic testing, testing providerused, test method, such as genetic sequencing method or gene panel, generesults, such as included genes, variants, expression levels/statuses,tumor mutational burden, and microsatellite instability. One type ofgenetic testing may be next-generation sequencing (NGS). Theabove-provided examples, enumerations, and lists are not intended tolimit the scope of the available fields and are intended to berepresentative of the nature and structure that fields may take.

In some instances, the application may direct a user to scan additionalpages of the document based on the predefined model associated with therecognized document identifier. For example, if a 20-page reportfeatures key health information on pages 1-5 and 17, the application maydetermine the format of the report and request the user to process anelectronic document capture on each of pages 1-5 and 17 beforeperforming additional data extraction. In another example, if a reporthas a non-standard page layout, the application may request the user toskip background sections, waivers, privacy notices, or other pages whichdo not contain key health information when capturing pages of thedocument. Exemplary key health information may be found in features ofthe document such as headers and tables. An exemplary header may includea standardized format with key health information such as a patient'sname, date of birth, age, gender, diagnosis, treating facility, andother medical data detailed above. An exemplary table may also includekey health information in the form of report summary information such asmutations or genetic variants identified during sequencing of apatient's DNA or gene expression counts identified during sequencing ofa patient's RNA. Extraction techniques are discussed in more detailbelow.

In another embodiment, the electronic document capture may reference thepredefined model to identify the region of the electronic documentcapture containing key health information and extract the identifiedregion for further processing. A region (such as a header, table,graphic, or chart) may be identified by utilizing a stored feature listfor the document, or each page of the document, that identifies featurespresent in the page along with their corresponding locations in thepage. For example, the model may indicate that a page should expect topresent a patient header, two tables, a chart, and a graph. A regionmask may be applied to the capture to verify that any regions expectedto be present are actually within the capture. A region to extract maybe identified by the region mask and, upon verifying that the region ispresent, the region may be extracted. Text may be identified from theextracted region and provided to a natural language processing (NLP)algorithm to extract patient information, such as patient name,diagnosis, notable genetic mutations, or gene expression countinformation including count values representing the number of times theRNA sequence occurs in sequencing and/or deviation in gene expressioncounts compared to the gene expression counts of normal samples that maybe labeled over or under expressed. More details for feature/regiondetection and extraction are discussed below with respect to tabularextraction.

Each field of the extracted region may have a plurality of enumeratedvalues, or, if an enumerated list of values is unavailable may belimited to a certain type of value. For example, if the field relates topatient diagnosis, it may have a corresponding enumerated list of alldiagnoses that may be provided in the report. If the field relates to atreatment, it may have all known treatments and further parse the fieldto identify and enumerate unknown treatments. Alternatively, if thefield is a medication that the patient was prescribed, it may be limitedto a type, so that data parsed will be checked against known medicationsand, if necessary, add the parsed text to a medications database as anew entry of type medications. The types of field, their enumeratedvalues, or the classification associated with unknown values may bestored as part of the predefined model.

In an alternate embodiment, a tabular extraction method may be performedon the OCR output of the electronic document capture. Where the abovemethod requires that each document type has a predefined model in-placeto capture specific elements from the document, a tabular extractionapproach may process a document type without a predefined model andgenerate a model as an output of an algorithm, described in more detailwith respect to FIG. 3, below. For example, every report may includepatient information or demographics such as the patient's name, date ofbirth, diagnosis, or institution which may be automatically parsedwithout particular knowledge of the specific report. In addition,specific reports may be discernible contextually, for example, a geneticsequencing report may include listing of genes, mutations, variants, andexpressions which would indicate that the report may provide certainclassifications of patient information that should be extracted. A genefield may be tagged as required, as any sequencing report may presentthis information and a mutation, variant, or expression field may betagged as optional as different sequencing reports may present differingtypes of information (such as a DNA report may include mutations, butnot expression).

FIG. 3 depicts an exemplary tabular extraction approach involving masks1-3. In this example, the document 30 being extracted may be astandardized report, such as a report used by a physician or group ofphysicians, including patient onboarding forms, progress notes,pathology reports, and other standard documents. Standardization in thissituation may indicate that the reports are presented in a generalformat with regularly occurring fields (permanent or optional) populatedspecific to a patient. For example, a patient onboarding form may have aheader 32 (as shown in FIGS. 4A-B) which lists patient information suchas name, address, symptoms, medications. A progress note may have atable that allows the physician to catalog treatment options recommendedto the patient, treatment options which were pursued from a previousvisit, and any updates to the status of the patient relating to thetreatment options pursued. A pathology report may include a firstsection 34 listing a plurality of genetic variants that may be tested ina specific pathology assay and a second section 36, which may bedistinct from the first section, providing sequencing results for eachcorresponding genetic variant of the first section at a spatiallycorresponding location to the first section. Furthermore, some reportsmay feature tables, charts, or other sections 38 that may expand or besplit across multiple pages, similar to section 4 of Mask 3 (also shownin FIGS. 4A-B).

In this context, a MLA or a deep learning neural network (DLNN) may beutilized. The MLA may have been trained with a training dataset thatcomprises annotations for types of classification that may be performed.It should be understood that the terms MLA and DLNN are interchangeablethroughout this disclosure. Thus, a mention of MLA may include acorresponding DLNN or a mention of DLNN may include a corresponding MLA.A resulting ruleset or neural network may identify or recognize aplurality of features across a standardized report or other templatesignifying that a classification may be extracted from a specificsection of a particular report based at least in part on that extractionruleset. Exemplary metrics and features that may be applied arediscussed in more detail below.

As noted above, one type of document that the system may be configuredto capture is a genetic testing report and, in a particular aspect, anext generation sequencing (NGS) report. For example, once the mobiledevice captures the NGS report about a sequenced patient (for example,by generating an electronic document capture), the system may extractsome or all of the NGS medical information (such as patient information,genes, mutations, variants, or expression data) contained in thedocument. Using various OCR, MLA, and DLNN techniques, such as thosedescribed herein, that extracted information then may be stored in adatabase or other data repository, preferably in a structured format.

The system may be configured to recognize various types of NGS medicalinformation from the captured report. For example, the system may beconfigured to extract and recognize NGS medical information relevant toone or more diseases, including: cancer, diabetes, depression,cardiovascular disease, neurological disorders, infectious diseases,lupus, or endocrinology-related diseases. The NGS medical informationadditionally may include one or more of: somatic variants, germlinevariants, tumor mutation burden (TMB) values, microsatellite instability(MSI) values, therapy resistance values, organoid response values,epigenetic values, RNA expression values, locus-based somatic variants,and/or gene-based somatic variants. Still further, the NGS medicalinformation may focus on specific genetic mutations, such as a KRASmutation, a BRCA mutation, an EGFR mutation, a CYP2C19 mutation or othermutations, such as any of the genes referenced below.

Once the system extracts the NGS medical information, the system thenmay classify or correlate that information to other medical data, based,e.g., at least in part on the feature(s) from which it is extracted. Forexample, the system may correlate the NGS medical information to priortreatment data, including medication and/or chemotherapy data. Thesystem also may correlate the NGS medical information to prior outcomesdata, including survival, remission, and/or tumor progression data. Itwill be appreciated that the prior treatment and/or prior outcomes datamay be from the patient to whom the NGS medical information relates orfrom patients other than the sequenced patient.

Turning to FIGS. 4A-B, an exemplary NGS report featuring Sections 1-4 asdescribed in FIG. 3 may be processed by an MLA or DLNN to identifySection 1 as a header 32 which lists a plurality of features 40, such asa patient's name, date of birth, and diagnosis; the institution's nameand location; and the date of report, of data collection, etc. The MLAmay also identify extraction techniques to apply, such as use sentencesplitting algorithms to parse a plurality of sentences and then regularexpressions to match “Patient Name:”, “D.O.B.:”, “Diagnosis:”,“Collection Date:”, and “Institution:” or alternatively splitting thesentences on the colon (“:”) character and applying the first results toa patient name field, second results to a date of birth field, thirdresult to a diagnosis field, fourth result to a collection date field,and fifth result to institution name and location fields.

The MLA may identify Section 2 as a region 34 including a plurality offeatures 42, such as a listing of genetic mutations which are linked toSection 3. For example, within this other region 36, the MLA mayenumerate additional features 44, including all possible geneticmutations or variants that may occur in Section 2. Additionally oralternatively, the MLA may be trained to identify the word “Mutation”and then determine that the text immediately preceding or following thatword is a candidate for a possible mutation. In this regard, the systemmay utilize the nature of mutation descriptions, namely that manymutations are represented by unique alphanumeric phrases, such as“KRAS,” “BRAF,” and “PIK3CA” in FIG. 4A. Thus, when the MLA identifiesthese phrases, it may compare them against a database or dictionary orknown mutations such that, when one or more matches are found, the MLAmay be able to conclude with a high degree of confidence that the matchcorresponds to a possible mutation, in other words, a risk of a falsepositive is low. Still further, because the mutations of Section 2 arelinked to the variants in Section 3, the MLA may perform a two-waycross-check against the dictionary or database in the event that thetext extracted does not correspond to a known mutation or variant. Atwo-way cross-check may also be performed to another section within thereport such as an appendix or glossary. For example, if the system readthe mutation “KRAS” as “RRAS,” it would not find the latter mutation inits database or dictionary. At that point, the system may check itscorresponding variant—in this case, “Exon 2 100C→A,” determine thatthere is a match in the database or dictionary for that variant, anddetermine that the mutation corresponding to that variant is “KRAS.” Atthat point, the MLA may either accept the change automatically, or itmay do a comparison between the extracted term, such as “RRAS,” and thismatching term, “KRAS.” The MLA may rely on various comparators, such asthe number of characters in each term, the number of matching charactersin each term (such as the second character in each term is an “R,” thethird character in each term is an “A,” and the fourth character in eachterm is an “S”), a comparability score between the non-identicalcharacters (such as “K” and “R” may be given a higher comparabilityscore than “K” and “Q,” as the former set of characters more closelyresemble one another than the latter), or other comparators, in order todetermine a likelihood of match. If the match likelihood is above acertain threshold, the MLA then may conclude that the extracted termshould be modified to the matching term and will replace the termaccordingly.

Furthermore, the MLA may identify a number of fields that may beextracted in this section as a range of values. For example, if there isalways at least 1 mutation listed but never more than 9, the MLA mayidentify a range from 1-9 for extraction, similarly, if there are nomutations listed, the MLA may “tag,” or annotate, this field as optionaland include a range of 0-9 mutations for extraction.

The MLA may identify each row in Section 3 as a corresponding sequencingresult to the genetic mutation of Section 2 in the same row. Forexample, if there are three rows in Section 2 identifying KRAS, BRAF,and PIK3CA mutations, there should exist at least three rows in Section3 which feature corresponding variants to the KRAS, BRAF, and PIK3CAmutations, respectively. The MLA may identify column and row numbers orjust row numbers for the number of genetic mutations, variants, orexpressions to extract based upon the detected structure duringprocessing. It is possible that there may be more than one variantdetected for a given mutation. In that regard, different document typesmay report that information differently. For example, one type ofdocument may provide the information in a 1:1 fashion, such that theremay be two rows in Section 2 with the same mutation listed, each rowcorresponding to a unique variant in Section 3. Alternatively, adifferent document type may group all variants for a given mutation inthe same box in Section 2, those different variants separated by somekind of indicator, such as a comma, semicolon, colon, slash, backslash,new line, etc.

Lastly, the MLA may identify Section 4 as a region 38A a multi-pagetable in which its features 46A include summaries of conclusions madefrom the sequencing results of Sections 2 and 3. In this example,Section 4 spans multiple pages, and the system may recognize that theportion 38B of Section 4 on the second page (FIG. 4B) is a continuationof the portion of Section 4 on the first page, with additional features46B. For example, the MLA may recognize a width of the columns in bothof the portions and determine that the widths of the respective portionsof each column are the same, the first column in Section 4 in FIG. 4A isthe same width as the first column in FIG. 4B. In another instance, theportion at the top of the second page may include one or more headers,which the MLA may recognize as the same header(s) as the portion ofSection 4 at the bottom of the first page. In still another instance,the MLA may recognize other text (such as “Continued” or “Cont'd” or “ .. . ”), signaling that the portion at the top of the second page is acontinuation of Section 4.

The MLA may identify a column and row structure where column 1, rows 1-Ncorrespond to Rows 1-N of Section 2. The MLA may further indicate thatOCR results of the previous Sections may be verified by comparing withthe current section and vice versa. Furthermore, the MLA may identifythat Column 2 of Rows 1-N correspond to therapies of genetic mutationsdetected in Section 2 and that Column 3 or Rows 1-N identify whether thetherapies are approved for other cancer types. For example, if there arethree rows, an exemplary model may identify that for N rows, column-rowpair 1-1, 1-2, . . . 1-N, each identify a mutation; column-row pair 2-1,2-2, . . . 2-N, each identify a therapy for that mutation; andcolumn-row pair 3-1, 3-2, . . . 3-N, each identify if alternatecarcinomas may be treated with the therapy. Just as there may exist Nrows there may also exist some number, M, of columns such thatcolumn-row pairs M-1, M-2, . . . M-N exist and relationships between thecolumns and rows may be represented.

Alternatively, the discrete elements in one or more of the columns mayspan more than one row. For example, in FIGS. 4A-B, the therapies may bepresented as a class of therapy on a first row, such as “PI3KInhibitors;” followed by one or more specific therapies within thatclass, such as “Erlotinib” and “Gefitinib,” on separate, successiverows. The MLA may be trained to recognize that an indentation from onerow to the next may indicate such group/instance relationships, thatsuccessive lines with no indentation may signify a continuation of thetext of the first line, and/or that a certain minimum amount of whitespace between lines may signify a break from one class of therapies tothe next.

Each of the above identifications, validity checks, or otherdeterminations made by the MLA may be encoded and stored in thepredetermined model (or predefined model as discussed above) forreference during processing of a report sharing the same template. Inthis regard, the model may be considering an overarching rule set usedto identify a report or other document. The model may be generated fromthe MLA, from a human curation, or a combination thereof (such as an MLAmodel supplemented with additional human curation). Templates for eachdocument may be one component of the model, along with identifiers foreach template, regions or masks, features or fields and tools orinstructions for how to extract those features or fields and verify theaccuracy of that extraction, associated sub-fields, and rules fornormalization of those fields and sub-fields.

One exemplary technique to access the data within each of the identifiedsections may be to generate a mask which “outlines” the section, applythe mask to the document to extract each section in turn, and thenprovide the section to an OCR algorithm, such as an OCR post-processingoptimized to extracting information from the respective section type.

As discussed above, exemplary masks for extracting each of the Sections1-4 are disclosed in FIG. 3. Mask 1 may identify the bounds of Section1, for example, by identifying a size (such as number of pixels, width,length, diameter, etc.), shape (such as square, rectangle, or othershape), and origin point (such as a pixel X,Y pair) for a mask 50A or byidentifying a starting (such as the pixel location of the top, leftside) and ending point (such as a pixel location of the bottom, rightside) of a rectangular mask. Other field designations may be useful forother shapes, for example, a circle may have an origin and a diameter,or any enclosed shape (polygonal or combinations of shapes), such as anL shaped box may have multiple corner points outlining the exterior ofthe mask in a node/edge graph relationship establishing nodes, edgesshared between nodes, and the location of each node. The mask may be anumerical 1 for the white region or 0 for the black region.Alternatively, the mask may be 1 for a pixel intensity value greaterthan/greater than or equal to a certain threshold and 0 for a pixelintensity less than or equal to/less than a certain threshold. The pixelvalues of the document then may be multiplied with the correspondingmask value to apply the mask or may be applied in a binary fashion suchas a logical AND operation. For example, only the region of the imagewhich is multiplied, or logical AND operation, with a 1 are kept forOCR; the region that is multiplied, or logical AND operation, with a 0is lost. Once the mask is applied, an exemplary optimized OCRpost-processing for that section may include a regular expression, suchas a regular expression or matching a string “Name:” or “DOB:”, and/or acolumn, row pair(s) which contains key health information, for example,a cell located at Column 2, Row 2 may provide a patient name, or a celllocated at Column 2, Row 3 may provide a patient date of birth. In asimilar fashion, Section 2 may be extracted next using a second mask 50Band Section 3 may be extracted using a third mask 50C. Sections 2 and 3may then be supplied to OCR post-processing for linking the results ofSection 3 to the enumerated content of Section 2. In an alternateembodiment, Sections 2 and 3 may be extracted at the same time using acombined mask 50D. Section 4 may similarly be extracted at the same timeusing a combined mask 50E by appending/concatenating the image of page 1and page 2 together or may be masked individually for each page and theresulting masked sections may be appended/concatenated for postprocessing. In other alternative embodiments, masking may be performedby cropping the image, extracting only the image along a bounded box, orother image segmentation techniques.

As discussed above, the MLA may search for one or more keywords orphrases identifying the entity generating the document, such as the“Institution:” keyword in Section 1 may trigger the MLA to understandthat the word or words following the “:” are an indicator of documentsource. The MLA then may use that information, alone or in combinationwith other extracted data such as the Collection Date value, a VersionNo., etc., to access a stored library of templates. For example, withregard to FIG. 4, the system may include one or more stored documenttemplates for documents created by “ABC Labs,” and the Oct. 20, 2018,collection date may inform the MLA as to which document to use whenthere are multiple documents.

The MLA or DLNN performing tabular extraction may be implemented as asingle training set for all documents, or it may be segmented into oneor more layers to improve processing speed of the each stage of theextraction process and to allow modular improvements to be incorporatedwithout retraining the entire process at once. An exemplary multi-layerextraction may be performed through a template-based approach using asupervised or semi-supervised training set or may be performed through afully tabular approach using an unsupervised or semi-supervised trainingset. In an exemplary template-based approach, an MLA may be providedwith specific forms containing a standardized layout for each documenttype commonly found in electronic document captures. Additionalinformation on how to identify the form may be provided (such as alocation/bound to OCR and a text string to match a document name). Inanother embodiment, the MLA may train to discern how to identify theform and may train to recognize concept candidates in the specific formdocument provided. The template-based approach (as described above) mayfurther incorporate the methods and processes of the instant tabularapproach to operate consistent with the below description.

In an exemplary tabular approach, a first layer of a multi-layered MLAmay process (in training) electronic medical record (EMR) and electronichealth record (EHR) documents to identify documents of similar form,layout, or structure. For example, in an EMR of a 1000 documents, thefirst layer MLA may identify that 400 of the documents follow a firstsimilar form (such as the document in FIG. 4 for the form in FIG. 3),300 follow a second similar form different from the first, and theremaining documents do not follow a similar form. The MLA may identifyone or more of a first subset of masks for the 400 documents of firstsimilar form (such as Sections 1-4 of FIG. 3) and may identify one ormore of a second subset of masks for the 300 documents of a secondsimilar form. An output of the MLA from the first layer may be a seriesof masks for each of the identified similar forms. In anotherembodiment, the first layer may be broken up into a series of MLA; forexample, the processing flow of the first layer may be arranged todivide the tasks of recognizing similar documents to identify apotential template and then process each template to generate masks foreach of the identified templates as two or more operations. The resultsof each layer of the MLA processing may be encoded into the predefinedmodel for retrieval during processing or may be encoded in the neuralnetwork of the DLNN.

A second layer of a multi-layered MLA then may utilize the resultingmasks from the first layer to process the training data set byidentifying regions of interest in a document, identifying acorresponding mask for each identified region of interest, and applyingthe mask to each document to extract and process the region of interest.An exemplary intermediary processing step of the second layer MLA mayidentify, for each region of interest, which type of feature the regionof interest may contain (such as a table, header, graph, etc.). Anoutput of the MLA from the second layer may be a series of masked imagesfor each of the regions of interest and an indicator for the type offeature that exists in the region of interest.

In another embodiment, the second layer may be broken up (orconsolidated) into a different series of MLA; for example, theprocessing flow of the second layer may be arranged to divide the tasksof applying each mask to each region of interest and identifying thefeatures of the region of interest into a single operation or furthersubdivide the processing into further operations.

A third layer of a multi-layered MLA may utilize the resulting maskedregions of interest and identified features for each region to select anoptimized OCR post-processing to extract the text from the region ofinterest. An exemplary optimized OCR post-processing for that sectionmay include a regular expression, such as a regular expression ormatching a string “Name:” or “DOB:”, and/or a column, row pair(s) whichcontains key health information, for example, a cell located at Column2, Row 2 may provide a patient name, or a cell located at Column 2, Row3 may provide a patient date of birth. Further post processing of theOCR text may identify that regions of interest are related to oneanother. For example, a first region of interest may provide a series ofgene variants while a second region of interest may provide theexpression level/status of those gene variants. In this example, thereare a known number of genes, each having a plurality of possiblevariants, and a query to a molecular pathology service may be initiatedto validate whether a recognized gene and variant combination isvalid/known or if the combination is actually an unrecognized variant,an OCR introduced error, or if the unknown combination originated fromthe document. The MLA may detect that regions are related and assign acorresponding concept candidate using both of the regions of interesttogether. By utilizing relationships between regions of interest in thedocument, the MLA may provide a more robust classification and provide amore detailed error checking than an algorithm that analyzes portions ofthe document in isolation. Related regions may further be used toprovide error correction or OCR validation. For example, certain reportsmay include a feature that includes genetic variations that have beenoverexpressed in an RNA report. A second feature nearby may representthe same overexpressed genetic variants but further provide therapiestargeting these genetic variants, and potential clinical trials that maybe relevant. The reuse of data in subsequent features provides anopportunity for validating correct OCR results by comparing the resultsfrom each of these respective features. In another example, an appendixmay be included at the end of the report that provides all variantswhich may be included. If an OCR error of a variant has occurred, thenthat result may not match any entry in the appendix, and may becorrected.

An unrecognized variant is one that has not been identified,sufficiently classified, or expertly-curated by the scientificcommunity. Generally, reports include only known variants and publishupdated documentation for any newly supported variants for eachtest/report offered. An output of the MLA from the third layer may be acollection of concept candidates or classifications for thedocument/patient. In another embodiment, the third layer may be brokenup (or consolidated) into different a series of MLAs; for example, theprocessing flow of the third layer may be arranged to divide the tasksof text extraction, classification, and identifying relationshipsbetween regions of interest into a single operation or further subdividethe processing into further operations.

While the instant embodiments are described as including three layerswith respective intermediate processing steps, it should be understoodthat each layer and the included intermediate processing steps may bereordered, combined, or skipped based on the layout of the trainingdocuments and configuration of the MLA. Therefore embodiments havingfewer or extra layers may be realized without departing from the spiritof the disclosure. Furthermore, the outputs of each layer of the MLA maybe encoded as rules in the predefined model for retrieval duringprocessing of a new document.

Identifying regions of interest, features within the region of interest,or relationships between regions may be performed from the OCR textitself or processed from the image itself prior to OCR. For example,identifying a region of interest may be performed by identifying aborder (such as a black box) that encapsulates some segment of text. Insome instances, a border may actually be identified using the negativespace (such as the white space) around a text by observing that thewhite space is of at least a uniform distance all around a segment oftext and creating a natural boundary. For example, white space that alsoborders an edge of a paper may be several times as thick as the whitespace above and below the segment of text, but there will be at least auniform white space of the width above and below, that is also presentin the larger section on the border. Other distinctions may be observedand utilized as well based on the MLA applied. For example, a table maybe identified by observing two or more intersecting lines. Similarly,lines segmenting the columns and rows of a table may be solid, dashed,or even extrapolated from the negative space between the words.Additionally or alternatively, OCR post-processing may recognize textwhich is presented in columns to combine the text in the correct order.Certain features may be identified based on the image of the text priorto OCR. For example, text in all capital letters may be identified byhaving more straight lines than typical text, bold text may beidentified by having thicker letters than typical text, or italicizedtext may be identified by have angled lines more frequently than typicaltext. These features of text may be applied in determining regions ofinterest, related regions, or concept candidates from each region ofinterest. Furthermore, features of text may be identified by both imagedetails (such as pixel density, pixel chroma, etc.) and text (such asthe OCRed words themselves are shared between documents). It isappreciated that MLA and DLNN may identify features, relationships, andmasks using any number of techniques which may not be easily predictedor explained herein, the above examples are merely exemplary, and easilyidentified/understood to illustrate the types of features that may beimportant to the MLA and DLNN but are not a full accounting of thepossibilities.

An exemplary natural language processing (NLP) algorithm may receive asan input, a region of the electronic document capture which has hadoptical character recognition (OCR) performed on the extracted region toidentify if the text of the region corresponds to the value typeexpected in that extracted region where the mask was applied. Forexample, if the region was expected to provide treatment information,the NLP algorithm may attempt to classify the extracted text astreatment information based off of the NLP algorithm training data set.Furthermore, the patient information being extracted, such as patientname, diagnosis, treatment, or sequencing information, may be associatedwith a respective field in the application. Extracted patientinformation may then be populated into the mobile application for reviewby the user, as seen in FIG. 16 and as discussed in greater detailbelow. The user may correct any errors by selecting the data field inthe application corresponding to the information. These errors may bestored and/or sent to a training engine to improve upon the extractionalgorithms and techniques. The training engine may generate a newextraction algorithm to use in future extractions based from detectederrors. More information is disclosed below with respect to FIGS. 8 and11, below. For text based fields, a text editor/keyboard may bedisplayed for the user to provide text corrections. Additionally,suggested replacements may also appear in a dropdown list in addition toor in place of the text editor. For date based fields, a calendar may bedisplayed to select the correct date, or for diagnosis, a drop downfeaturing diagnoses supported by the document type, report type, or eventhe database may be enumerated for selection. The field types listedabove are merely representative and are not intended to limit fields tothe specific type of data associated in the above description, forexample, date based fields may also be populated using text input. Thepredefined model that is associated with each of the templates maycontain reference fields to identify each of the fields that may beextracted to generate the extracted patient information. For example, afeature corresponding to the informational header may have acorresponding field in the predefined model which lists a location thepatient name is expected, a location the patient date of birth isexpected, and a location of the diagnosis (such as cancer type) isexpected as described above.

In an alternative embodiment, a MLA may receive as an input, a region ofthe electronic document capture which has had optical characterrecognition (OCR) performed on the extracted region to identify if thetext of the region corresponds to the value type expected in thatextracted region where the mask was applied. For example, if the regionwas expected to provide treatment information, the MLA may attempt toclassify the extracted text as treatment information based off of theMLA training set. Furthermore, the patient information being extracted,such as a patient name, diagnosis, treatment, or sequencing information,may be associated with a respective field in the application. Extractedpatient information may then be populated into the mobile user interfacefor review by the user. Other information that may be extracted mayinclude: gene(s) (such as TP53, NF1, or PDL1); gene expression countinformation (such as over/under expressed or count values representingthe number of times the expression occurs in sequencing); respectivegene variants (such as Q192 or E496); gene variant calls (such as“4724+1G>A”, “Q192*”, or “c.380C>A”); depth of sequencing (such asoccurrences of chromosome hits per number of DNA reads); scope ofsequencing (such as panel type: whole genome or targeted panels);proteomics (such as protein based assertions: counts and shapes);epigenetics; RNA expressions (such as over-expression orunder-expression); organoids (such as chemical/medical responsesorganoids experienced in a lab setting); germline (such as mutationspresent in healthy cell DNA); immunotherapies (such as engineered immunereceptors such as CAR-T, cancer vaccines, checkpoint blockades, etc.);and tumor-normal (such as a comparison of RNA and/or DNA sequencingresults of tumor tissue with RNA and/or DNA sequencing results of anon-tumor sample, such as non-tumor tissue, blood, or saliva). Featuresof the electronic data capture may also be directed to clinical trials,for example, by listing details associated with the name of the clinicaltrial, geographic location of the facilities administering the trial,treatments associated with the trial, inclusion/exclusion criteria forpatients who may participate in the trial, and other relevantinformation.

Information that is extracted may be from various disease states andrelate to various genes or locus/loci (a fixed position on a chromosome,such as the position of the gene or genetic marker). For instance, on areport providing genetic sequencing information that may help aclinician make a decision about which medication to prescribe for apatient's depression, the genes related to the information on the reportmay include one or more of CYP2C19, CYP2D6+DEL/DUP, CYP1A2, CYP2B6,CYP2C9, CYP3A4, HLA-A, HLA-B, HTR2A, SLC6A4, or UGT1A4. In otherexamples, the genes related to the information on the report may includeone or more of 5HT2C, ABCB1 (MDR1), ABCG2, ACE, ADRA2A, ADRB1, ADRB2,AGT, ANKK1, ANK3, APOE, BDNF, CACNA1C, CES1, COMT, CYP3A5, CYP4F2, DPYD,DRD1, DRD2, DRD3, EDN1, ERCC1, FCGR2A, FCGR3A, F2, F5, G6PD, GNB3,GRIK1, GRIK4, GSTP1, HNF4A, HSD3B1, HTR2C, HTR1A, IFNL3, IL28B (IFNL4),KCNIP1, KCNJ11, KCNQ1, LDLR, LIPC, MC4R, MTHFR, MTRR, NEUROD1/BETA2,NQO1, NR1H3, NUDT15, OPRM1, PAX4, POLG, PPARA, PPARG2, PPARGC1A, PRKAA1,PRKAB2, PTPRD, RBP4, SLC6A2, SLC22A1 (OCT1), SLC22A2 (OCT2), SLC30A8,SLC49A4 (PMAT), SLC47A1 (MATE1), SLC47A2 (MATE2-K), SLCO1B1, SOD2,STK11, TCF7L2, TPMT, TYMS, UCP2, UGT1A1, UGT1A9, UMPS, or VKORC1.

In other examples, the genes related to the information on the reportmay include one or more of AATK, ABCA1, ABCB1, ABCB11, ABCB4, ABCC1,ABCC2, ABCG1, ABCG2, ABI1, ABL1, ABL2, ACE, ACSL6, ACTA2, ACTC1, ACVR1,ACVR1B, ACVR2A, ACVR2B, ADAM17, ADAMTS20, ADGRA2, ADGRB3, ADGRL2,ADGRL3, ADRB1, ADRB2, AFF1, AFF2, AFF3, AHR, AIP, AJUBA, AKAP9, AKT1,AKT2, AKT3, ALK, ALKBH6, ALOX12B, ALOX5, AMER1, APC, APEX1, APH1A,APOA1, APOB, AR, ARAF, AREG, ARFRP1, ARHGAP10, ARHGAP26, ARHGAP35,ARID1A, ARID1B, ARID2, ARID5B, ARNT, ARNT2, ARPC1A, ARPC1B, ARTN, ARX,ASCL1, ASCL2, ASCL3, ASCL4, ASCL5, ASH1L, ASH2L, ASPSCR1, ASXL1, ASXL2,ASXL3, ATAD2, ATAD2B, ATF1, ATM, ATR, ATRX, AURKA, AURKB, AURKC, AXIN1,AXIN2, AXL, B2M, BABAM1, BACH1, BACH2, BAG4, BAP1, BARD1, BAX, BAZ1A,BAZ1B, BAZ2A, BAZ2B, BBC3, BCAR3, BCL10, BCL11A, BCL11B, BCL2, BCL2A1,BCL2L1, BCL2L11, BCL2L2, BCL3, BCL6, BCL7A, BCL9, BCLAF1, BCOR, BCORL1,BCR, BDNF, BID, BIRC2, BIRC3, BIRC5, BIRC8, BLK, BLM, BLNK, BMI1,BMPR1A, BMPR1B, BMX, BPTF, BRAF, BRCA1, BRCA2, BRD1, BRD2, BRD3, BRD4,BRD7, BRD8, BRD9, BRDT, BRIP1, BRPF1, BRPF3, BRWD1, BRWD3, BTC, BTG1,BTG2, BTG3, BTK, BTRC, BUB1, BUB1B, BUB3, CACNA1C, CACNA1S, CACNB2,CADM2, CALR, CAMTA1, CAPRIN2, CARD10, CARD11, CARD6, CARDS, CARM1,CASC11, CASP8, CBFA2T2, CBFA2T3, CBFB, CBL, CBLB, CBLC, CBX1, CBX2,CBX3, CBX4, CBX5, CBX6, CBX7, CBX8, CCDC6, CCNB3, CCND1, CCND2, CCND3,CCNE1, CCNE2, CCNL1, CD1D, CD22, CD274, CD276, CD28, CD40, CD40LG, CD44,CD70, CD79A, CD79B, CD80, CD86, CDC14A, CDC20, CDC25A, CDC25B, CDC25C,CDC42, CDC6, CDC73, CDH1, CDH10, CDH11, CDH2, CDH20, CDH3, CDH5, CDH7,CDK1, CDK10, CDK11A, CDK11B, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17,CDK18, CDK19, CDK2, CDK20, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9,CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN3, CDX1, CDX2,CEBPA, CEBPB, CEBPD, CEBPE, CEBPG, CEBPZ, CECR2, CENPE, CES1, CES2,CHD1, CHD1L, CHD2, CHD3, CHD4, CHD5, CHD6, CHD7, CHD9, CHEK1, CHEK2,CHIC1, CHIC2, CHUK, CIC, CIITA, CKS1B, CKS2, CLIP1, CMPK1, CNKSR1,CNOT3, CNTFR, COL3A1, COMT, COPS3, CRBN, CREB1, CREB3L1, CREB3L2,CREB3L4, CREBBP, CREM, CRHR1, CRK, CRKL, CRLF2, CRTC1, CRTC2, CRTC3,CSF1, CSF1R, CSF2RA, CSF2RB, CSF3R, CSK, CSNK1D, CSNK1E, CTCF, CTCFL,CTLA4, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTNND1, CTSD, CTSL, CTSS, CUL3,CUL4A, CUL4B, CUX1, CYLD, CYP17A1, CYP1A2, CYP21A2, CYP2A6, CYP2B6,CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2J2, CYP2R1, CYP3A4, CYP3A5, CYP4F2,DACH1, DACH2, DAXX, DBH, DCC, DCUN1D1, DCUN1D2, DDB2, DDIT3, DDR1, DDR2,DDX3X, DDX5, DDX6, DEK, DHFR, DHH, DIAPH1, DIAPH2, DIAPH3, DICER1,DIRAS3, DIS3, DKC1, DMXL1, DNM2, DNMT1, DNMT3A, DNMT3B, DNMT3L, DOCK2,DOT1L, DPYD, DRD1, DRD2, DSC2, DSG2, DSP, DUSP22, DVL1, DVL2, DVL3,DYRK2, E2F1, E2F3, E2F5, E2F6, E2F7, EBF1, ECT2L, EED, EGF, EGFR, EGR1,EGR2, EHF, EHMT1, EHMT2, EIF1AX, ELANE, ELF1, ELF2, ELF3, ELF4, ELF5,ELK1, ELK3, ELK4, ELP3, EML4, EMSY, EP300, EPCAM, EPGN, EPHA1, EPHA2,EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB4,EPHB6, EPOR, ERBB2, ERBB3, ERBB4, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5,EREG, ERF, ERG, ESCO1, ESCO2, ESPL1, ESR1, ESR2, ESRRA, ETS1, ETS2,ETV1, ETV2, ETV3, ETV3L, ETV4, ETV5, ETV6, ETV7, EWSR1, EXT1, EXT2,EXTL1, EZH1, EZH2, FADD, FAM175A, FAM46C, FANCA, FANCB, FANCC, FANCD2,FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAS, FASLG, FAT1, FAT2, FAT3,FAT4, FBN1, FBXO11, FBXO8, FBXW11, FBXW7, FEN1, FER, FES, FEV, FGF1,FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2,FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9,FGFR1, FGFR2, FGFR3, FGFR4, FGR, FH, FHIT, FIGF, FKBP10, FKBP5, FKBP9,FLCN, FLI1, FLT1, FLT3, FLT3LG, FLT4, FOLH1, FOS, FOSB, FOSL1, FOSL2,FOXA1, FOXA2, FOXA3, FOXG1, FOXL1, FOXL2, FOXM1, FOXN3, FOXO1, FOXO3,FOXO4, FOXP1, FOXP2, FOXP3, FOXP4, FOXQ1, FRK, FRS2, FRS3, FSHR, FUBP1,FUS, FYN, FZR1, G6PC3, G6PD, GAB1, GAB2, GABPA, GALNT12, GATA1, GATA2,GATA3, GATA5, GATA6, GDNF, GFI1, GFI1B, GFRA4, GGCX, GHR, GID4, GLA,GLCCI1, GLI1, GLI2, GLI3, GLIS1, GLIS2, GLIS3, GNA11, GNA13, GNAQ, GNAS,GNRHR, GOT1, GPC3, GPC5, GPS2, GRB10, GRB2, GRB7, GREM1, GRIN2A, GRK4,GRK5, GRM3, GRM8, GSK3A, GSK3B, GSTT1, GTPBP4, GUCY1A2, H3F3A, HAX1,HBEGF, HCK, HDAC1, HDAC10, HDAC11, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6,HDAC7, HDAC8, HDAC9, HDGF, HELLS, HES1, HES2, HES4, HEY1, HEY2, HGF,HIF1A, HIF1AN, HIST1H1E, HIST1H3B, HIST1H4E, HLA-A, HLA-B, HLF, HLTF,HMGA1, HMGA2, HMGCR, HNF1A, HNF1B, HNRNPA3, HOXA10, HOXA11, HOXA13,HOXA3, HOXA9, HOXB13, HOXB3, HOXC10, HOXC11, HOXC13, HOXD10, HOXD11,HOXD13, HOXD3, HOXD4, HR, HRAS, HSD11B2, HSD3B1, HSP90AA1, HSP90AB1,HSPBAP1, HTR1A, HTR2A, ICK, ICOS, ICOSLG, ID1, ID2, ID3, ID4, IDH1,IDH2, IFNLR1, IGF1, IGF1R, IGF2, IGF2R, IHH, IKBIP, IKBKAP, IKBKB,IKBKE, IKZF1, IKZF2, IKZF3, IL10RA, IL10RB, IL11RA, IL12RB1, IL12RB2,IL13RA1, IL15RA, IL17RA, IL17RB, IL17RC, IL18R1, IL18RAP, IL1R1, IL1R2,IL1RAP, IL20RA, IL20RB, IL21R, IL22RA1, IL22RA2, IL23R, IL2RA, IL2RB,IL2RG, IL3, IL3RA, IL4R, IL5RA, IL6R, IL6ST, IL7R, IL9R, ING1, ING4,INHBA, INPP4B, INSR, INSRR, INTS12, IQGAP1, IQGAP2, IQGAP3, IRAK1, IRF4,IRF5, IRF6, IRS1, IRS2, IRS4, ITK, ITPKB, JADE1, JAK1, JAK2, JAK3,JARID2, JAZFl, JMJD1C, JMJD4, JMJD6, JMJD7, JMJD8, JUN, JUNB, JUND, JUP,KAT2A, KAT2B, KAT5, KAT6A, KAT6B, KAT7, KATE, KCNH2, KCNJ5, KCNQ1,KDM1A, KDM1B, KDM2A, KDM2B, KDM3A, KDM3B, KDM4A, KDM4B, KDM4C, KDM4D,KDM5A, KDM5B, KDM5C, KDM5D, KDM6A, KDM6B, KDM7A, KDM8, KDR, KDSR, KEAP1,KEL, KHSRP, KIF1B, KIT, KITLG, KLF12, KLF4, KLF5, KLF6, KLF8, KMT2A,KMT2B, KMT2C, KMT2D, KMT2E, KRAS, LATS1, LATS2, LCK, LDB1, LDLR, LEF1,LEPR, LGR4, LGR5, LGR6, LHCGR, LIFR, LMNA, LMO1, LMO2, LMO7, LMTK2,LMTK3, LPP, LRP1B, LRP5, LRP6, LRRK2, LSM1, LTK, LYL1, LYN, LZTR1,MAD1L1, MAD2L1, MAD2L2, MAF, MAFB, MAGED1, MAGI2, MAK, MALT1, MAML1,MAML2, MAML3, MAMLD1, MAOA, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5,MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K14,MAP3K15, MAP3K19, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7,MAP3K8, MAP3K9, MAP4, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAP4K5, MAPK1,MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK15, MAPK3, MAPK4, MAPK6,MAPK7, MAPK8, MAPK9, MAST1, MAST2, MATK, MAU2, MAX, MBD1, MBD3, MC1R,MCL1, MCPH1, MDM2, MDM4, MDS2, MECOM, MED12, MED12L, MED29, MEF2B, MEN1,MERTK, MET, MGA, MGMT, MIDI, MINK1, MIPOL1, MITF, MKL1, MKL2, MLF1,MLH1, MLH3, MLLT1, MLLT10, MLLT11, MLLT3, MLLT6, MLST8, MN1, MNX1,MOB1A, MOB1B, MOS, MPG, MPL, MRE11A, MSH2, MSH3, MSH4, MSH6, MSI2, MST1,MST1R, MTAP, MTCP1, MTDH, MTOR, MUSK, MUTYH, MXD1, MYB, MYBL1, MYBL2,MYBPC3, MYC, MYCL, MYCN, MYD88, MYH11, MYH7, MYL2, MYL3, MYLK, MY0D1,NA, NAB1, NAB2, NAT2, NBN, NCK1, NCK2, NCOA1, NCOA2, NCOA3, NCOA4,NCOR1, NCOR2, NCSTN, NDRG1, NEK1, NEK10, NEK11, NEK2, NEK3, NEK4, NEK5,NEK6, NEK7, NEK8, NEK9, NF1, NF2, NFATC1, NFATC2, NFATC3, NFATC4,NFE2L2, NFIA, NFIB, NFIC, NFIX, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBID,NFKBIE, NFKBIZ, NGF, NHP2, NIPBL, NKX2-1, NKX2-2, NKX2-3, NKX2-4,NKX2-5, NKX2-6, NKX2-8, NKX3-1, NKX3-2, NLRP1, NOD2, NONO, NOP10,NOTCH1, NOTCH2, NOTCH2NL, NOTCH3, NOTCH4, NPM1, NPPB, NPR1, NQO1, NR0B1,NR3C1, NR3C2, NR4A1, NR4A2, NR4A3, NRAS, NRG1, NRG2, NRG3, NRG4, NRIP1,NRTN, NSD1, NT5C2, NTF3, NTF4, NTRK1, NTRK2, NTRK3, NUMB, NUMBL, NUP214,NUP93, NUP98, NUTM1, NUTM2A, NUTM2B, NUTM2F, NUTM2G, ODC1, OLIG2, OSMR,PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PALB2, PALLD, PARK2, PARP1, PARP2,PARP4, PATZ1, PAX1, PAX2, PAX3, PAX4, PAX5, PAX6, PAX7, PAX8, PAX9,PAXIP1, PBRM1, PBX1, PBX2, PBX3, PBX4, PCBP1, PCSK9, PDCD1, PDCD1LG2,PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDK1, PDPK1, PDS5A, PDS5B,PEAR1, PEG3, PERP, PGF, PGR, PHB, PHF1, PHF2, PHF6, PHF8, PHIP, PHLPP1,PHLPP2, PHOX2A, PHOX2B, PICALM, PIK3C2A, PIK3C2B, PIK3C2G, PIK3C3,PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R4, PIM1,PIM2, PIM3, PKHD1, PKP2, PLA2G2A, PLAG1, PLAGL1, PLAGL2, PLCG1, PLCG2,PLK1, PLK2, PLK3, PLK4, PMAIP1, PML, PMS1, PMS2, PNRC1, POLD1, POLE,POR, POT1, POU2AF1, POU2F2, POU5F1, POU5F1B, POU5F2, POU6F1, POU6F2,PPARA, PPARD, PPARG, PPFIA1, PPM1D, PPP1R1C, PPP2R1A, PPP2R1B, PPP2R2B,PPP6C, PRCC, PRDM1, PRDM10, PRDM11, PRDM12, PRDM13, PRDM14, PRDM15,PRDM16, PRDM2, PRDM4, PRDM5, PRDM6, PRDM7, PRDM8, PRDM9, PREX2, PRF1,PRKACA, PRKACB, PRKAG2, PRKAR1A, PRKAR1B, PRKCI, PRKD1, PRKDC, PRLR,PRMT1, PRMT2, PRMT3, PRMT5, PRMT6, PRMT7, PRMT8, PRPF40B, PRPF6, PRRX1,PRRX2, PRSSl, PRSS3, PRSS8, PSEN1, PSEN2, PSENEN, PSIP1, PSPN, PTCH1,PTCH2, PTEN, PTGIS, PTGS1, PTGS2, PTK2, PTK2B, PTK6, PTK7, PTPN11,PTPN2, PTPN21, PTPN6, PTPRB, PTPRC, PTPRD, PTPRF, PTPRG, PTPRJ, PTPRK,PTPRM, PTPRQ, PTPRR, PTPRT, PTTG1, PVT1, RAB23, RAB25, RABEP1, RAC1,RAC2, RAD21, RAD50, RAD51, RAD51AP1, RAD51B, RAD51C, RAD51D, RAD52,RAD54B, RAD54L, RAF1, RAP1GDS1, RARA, RARB, RARG, RASA1, RB1, RBM10,RBM14, RBM15, RBMX, RBMXL1, RBMXL2, RBPJ, REC8, RECQL4, REL, RELA, RELB,RET, RHEB, RHOA, RHOB, RHOH, RHOT1, RICTOR, RIPK1, RIPK2, RIPK3, RIPK4,RIT1, RNF213, RNF40, RNF43, ROBO2, ROCK1, ROCK2, ROR1, ROR2, ROS1, RPA1,RPL5, RPN1, RPS6KB1, RPS6KB2, RPTOR, RRM1, RSPO2, RSPO3, RUNX1, RUNX1T1,RUNX2, RUNX3, RUVBL1, RXRA, RYK, RYR1, RYR2, SAMD9, SAV1, SBDS, SCN5A,SDHA, SDHAF2, SDHB, SDHC, SDHD, SET, SETBP1, SETD1A, SETD1B, SETD2,SETD3, SETD4, SETD5, SETD6, SETD7, SETD8, SETD9, SETDB1, SETDB2, SETMAR,SF1, SF3A1, SF3B1, SFPQ, SFRP1, SGK1, SGOL1, SGOL2, SH2B3, SH2D1A,SH3GL1, SHB, SHC1, SHC2, SHC3, SHC4, SHFM1, SHE, SHOC2, SKI, SKIL,SKOR1, SKP2, SLC15A2, SLC19A1, SLC22A1, SLC22A2, SLC22A3, SLC22A6,SLC26A3, SLC47A1, SLC47A2, SLC6A3, SLC6A4, SLCO1A2, SLCO1B1, SLCO1B3,SLCO2B1, SLIT2, SLX4, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, SMAD7,SMAD9, SMARCA1, SMARCA2, SMARCA4, SMARCA5, SMARCB1, SMARCC1, SMARCD1,SMARCD2, SMARCD3, SMARCE1, SMC1A, SMC1B, SMC2, SMC3, SMC4, SMC5, SMC6,SMCHD1, SMO, SMURF1, SMURF2, SMYD1, SMYD2, SMYD3, SMYD4, SMYD5, SOCS1,SOS1, SOS2, SOX1, SOX10, SOX17, SOX2, SOX21, SOX3, SOX8, SOX9, SP100,SP110, SP140, SP140L, SP3, SPDEF, SPEN, SPI1, SPI3, SPIC, SPOP, SPOPL,SPRED1, SPRED2, SPRED3, SPRY2, SPRY3, SRC, SRGAP3, SRMS, SRSF2, SS18,SS18L1, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, SSX1, SSX2, SSX3, SSX4,STAG1, STAG2, STARD3, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6,STK11, STK19, STK3, STK36, STK4, STYK1, SUFU, SULT1A1, SUV39H1, SUV39H2,SUV420H1, SUV420H2, SUZ12, SYK, SYNE1, TAF1, TAF15, TAF1L, TALI, TAL2,TAOK1, TAOK2, TAOK3, TBC1D12, TBL1X, TBL1XR1, TBP, TBX18, TBX2, TBX22,TBX3, TBXAS1, TCEB1, TCF12, TCF3, TCF4, TCF7, TCF7L1, TCF7L2, TCL1A,TCL1B, TEAD1, TEAD2, TEAD3, TEAD4, TEC, TEF, TEK, TENM2, TERC, TERF1,TERT, TET1, TET2, TET3, TFE3, TFEB, TFEC, TFG, TGFA, TGFB1, TGFB2,TGFBR1, TGFBR2, THPO, TIE1, TINF2, TLK1, TLK2, TLR1, TLR10, TLR2, TLR4,TLR5, TLR6, TLR7, TLR8, TLR9, TLX1, TLX2, TLX3, TMC6, TMC8, TMEM127,TMEM43, TMPRSS2, TNFAIP3, TNFRSF14, TNFRSF17, TNK1, TNK2, TNKS, TNKS2,TNNI3, TNNT2, TOP1, TOP2A, TOP2B, TP53, TP53BP1, TP63, TPM1, TPMT, TPTE,TPTE2, TRAF1, TRAF2, TRAF3, TRAF3IP1, TRAF3IP2, TRAF3IP3, TRAF6, TRAF7,TRIB1, TRIB2, TRIB3, TRIM24, TRIM28, TRIM33, TRIM66, TRIO, TRRAP, TSC1,TSC2, TSHR, TSHZ3, TWIST1, TWIST2, TXK, TYK2, TYRO3, U2AF1, U2AF2,UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE4A, UBR5, UGT1A1, UGT1A4, UHRF1,UHRF2, USB1, USP9X, USP9Y, UTY, VAV1, VAV2, VAV3, VDR, VEGFA, VEGFB,VEGFC, VGLL1, VGLL2, VGLL3, VGLL4, VHL, VHLL, VKORC1, VTCN1, WAPL, WAS,WASL, WHSC1, WHSC1L1, WIF1, WISP1, WNK1, WNK2, WNK3, WNK4, WNT1, WNT10A,WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B,WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B, WRN, WT1, WWTR1, XBP1,XIAP, XIRP2, XPA, XPC, XP01, XRCC2, YAP1, YEATS4, YES1, YWHAB, YWHAE,YWHAH, YWHAQ, YWHAZ, YY1, ZAP70, ZBTB16, ZBTB20, ZBTB33, ZBTB5, ZBTB7B,ZC3H12A, ZC3H12D, ZC3H7B, ZCCHC7, ZEB2, ZFHX3, ZMYM3, ZMYND11, ZMYND8,ZNF217, ZNF384, ZNF423, ZNF444, ZNF471, ZNF521, ZNF607, ZNF639, ZNF668,ZNF703, ZNF704, ZNF750, ZNRF3, or ZRSR2. In other examples, the genesrelated to the information on the report may include one or more ofgenes sequenced in a whole exome panel, which is a panel that sequencesthe whole exome. In other examples, the genes related to the informationon the report may include one or more of the genes sequenced in a wholegenome panel, which is a panel that sequences the whole genome.

For each feature, the list of fields may be retrieved from thepredefined model and candidate extraction may be performed according tothe expected field. Each candidate that is extracted using the methodsdetailed above may have a confidence value identifying an estimatedaccuracy of the result. In some circumstances, a high level ofconfidence may not be available. When a level of certainty lies below athreshold value (such as less than 90%), the MLA may output the highestentry with the highest level of certainty calculated identifying, forexample, a 60% confidence male and 40% confidence female. In anotherembodiment, no prediction may be generated when the confidence value isbelow the threshold and the user may be required to manually populatethe associated field in the application.

Extracted candidate concepts may be processed to identify any linksbetween the concepts and known entities, for example, the enumeratedlist of medical drugs discussed above. Entity linking is the task ofdetermining whether a candidate concept (phrase) is a relevant clinicalconcept. Relevancy may be determined by the presence of the candidateconcept in a medical dictionary. Fuzzy matching may be implemented by anapproximate string matching algorithm. For example, in conventionalstring matching, a string must exactly match, character for character,with a reference string in order to yield a positive match result. Infuzzy string matching a string is still matched character by character;however, for each mismatch in character, operations may be performed toelicit a match. For example, a mismatching character may be deleted, andthe next character considered for a hit, which would account for havingan extraneous character in a word, a character may be inserted at themismatching character to provide a match to allow a match to occur evenif a character was omitted, a character may be substituted at themismatching character to allow a match even if the wrong character wasinserted, or a character may be transposed at the mismatching character.For each mismatch operation that is performed, a counter may incrementto track the number of errors allowed. In an embodiment, the number oferrors may be capped to restrict the flexibility of the fuzzy searchingalgorithm, for example, only three mismatch corrections may be allowedbefore no match may be identified during processing. Other embodimentsmay adjust the threshold based upon the length of the word to allowlonger words more mismatches than shorter words. For example, if a threeletter word is allowed three mismatch operations, then a fuzzy stringmatching algorithm may generate matches for thousands of concepts from1-6 characters.

Fuzzy matching is structured around the text concepts included in themedical dictionary and may be applied on a word-by-word basis ratherthan a letter-by-letter basis. For example, a concept candidate mayinclude the phrase “needle biopsy.” An entity matching search mayidentify entities linked to, for example an exact match “needle biopsy”,a reordered match “biopsy needle”, or phrase matches of “needleaspiration biopsy of lung” or “breast needle biopsy.” Such entitymatches may be derived using the same fuzzy matching operations above(deletion, insertion, transcription, etc.), but on the whole word ratherthan each individual character. Furthermore, in still anotherembodiment, both fuzzy matching on a character by character basis andword by word basis may be applied concurrently to generate entitymatches.

Certain features, such as the TNM Classification of Malignant Tumors(TNM) or genetic variant/mutation results, may be preempted from fuzzymatching because the sequence of the characters are important and anyrearrangement or replacement (fuzzy matching) to generate a match maycause the incorrect concept to be matched.

Matched concepts may be normalized to ensure that the concepts that arematched are consistent with the concepts archived in the database(described below in more detail). For example, in a cancer typenormalization, there may be numerous candidate matches which referencebreast cancer in one form or another that match. A post-processing stepto the normalization may be applied which identifies, for example, whena cancer site is designated as breast, and adjusts the final result suchthat all entries with a breast cancer site share the same cancer sitecode and same spelling “breast”. Other normalized results may includeeach main cancer site, such as brain, lung, liver, ovary, or bonemarrow, a predetermined catch-all for unknown sites, or known codeswhich are irrelevant and may be filtered.

With regard to both the post-processing of scanned documents discussedabove, as well as the analysis and structuring of other aspects ofpatient EHRs or EMRs, such as next-generation sequencing reports, asystem that identifies and processes information in clinical documentsor other records is disclosed herein. The system may use a combinationof text extraction techniques, text cleaning techniques, naturallanguage processing techniques, machine learning algorithms, and medicalconcept (Entity) identification, normalization, and structuringtechniques. The system also maintains and utilizes a continuouscollection of training data across clinical use cases (such asdiagnoses, therapies, outcomes, genetic markers, etc.) that help toincrease both accuracy and reliability of predictions specific to apatient record. The system accelerates a structuring of clinical data ina patient's record. The system may execute subroutines that highlight,suggest, and pre-populate an electronic medical record (“EHR” or “EMR”).The system may provide other formats of structured clinical data, withrelevant medical concepts extracted from the text and documents ofrecord.

The system may include a persistent, stateless service that receives aplurality of queued messages from one or more peripheral services (suchas a file conversion service or an optical character recognitionservice) which may also perform natural language processing (NLP)operations on outputs of those peripheral services. Those NLP operationsinclude machine learning features, as described herein, in order toincrease the speed, efficiency, and accuracy of the processing. Apersistent, stateless system is a system operating in an asynchronousmanner in comparison to a conventional point to point pipeline. Forexample, the system may be structured in a “pipeline” fashion, but eachmodular component of the system may retrieve and store exemplaryinput/output datasets as they become available, without relying on themodular component before or after in the pipeline to initiate oracknowledge availability for a transfer. Such statelessness allows formore advanced parallelization because it reduces inefficiencies at eachbottleneck of the pipeline (handshaking to pass data). More detail onthe persistent, stateless service is discussed with reference to FIG. 5below.

The system may include a training service designed to promote userinteraction to improve machine learning capabilities. In one aspect, thetraining service may use a production repository as its input data. Inanother aspect, the training service may use a data repository separatefrom the production repository. Additionally, the system may operate ina plurality of manners. In a first manner, the system may be triggeredin response to specific queries requesting processing on specific EHR orEMR files. In a second manner, the system may include a backend servicethat reviews and processes EHR or EMR files continuously (without a needfor specific user queries). The backend service may operateasynchronously from user input, such as queries or commands. In such amanner, the system may detect when a patient record has been received,either partially or in full, and begin processing the patient record inaggregate or as a whole to determine relevant medical concepts for entryinto the EMR.

In the field of clinical abstraction from EHR and EMR documents, machinelearning or deep learning may be combined with NLP techniques toabstract relevant medical concepts. While the detailed implementationsof these are disclosed in more detail below, an exemplary abstractionperformed on a simple text is now provided to give a generalunderstanding of one aspect of the disclosure. For instance, the simpletext “The patient was given Tylenol 50 mg at 10:35 am.” may be analyzedusing a machine learning algorithm (MLA) trained on EHR and EMRdocuments relating to thousands of patients to recognize medicationsthat the patient was prescribed in order to generate the table 52 ofFIG. 6, where the MLA may be the same or a different MLA from the onediscussed above.

Generating a training set from which to train the MLA involves bothenumerating known drugs (which may include thousands or even tens ofthousands of drugs) and also maintaining the flexibility to recognizedrugs which are not included in the sources of the known drugs. Theprocess of enumerating the known drugs into a list may includeidentifying clinical drugs prescribed by healthcare providers,pharmaceutical companies, and research institutions. Such providers,companies, and institutions may provide reference lists of their drugs.For example, the US National Library of Medicine (NLM) publishes aUnified Medical Language System (UMLS) including a Metathesaurus havingdrug vocabularies including CPT®, ICD-10-CM, LOINC®, MeSH®, RxNorm, andSNOMED CT®. Each of these drug vocabularies highlights and enumeratesspecific collections of relevant drugs. Other institutions such asinsurance companies may also publish clinical drug lists providing alldrugs covered by their insurance plans. By aggregating the drug listingsfrom each of these providers, companies, and institutions, an enumeratedlist of clinical drugs that is universal in nature may be generated.

A combination of NLP and supervised, semi-supervised, or unsupervisedMLA techniques may be used to generate an intelligent training set ofdata to recognize entries from the enumerated list of clinical drugs, inorder to identify patterns within the text of abstracted documents whichtypically surround drug entries. The identified patterns may then beapplied to unknown drugs to generate new entries which are added to theclinical drug list. An exemplary pattern may be a sentence structurecontaining “patient was given ” or “patient was prescribed ______.” Inthese examples, the known drugs are the supervised portion of thesemi-supervised algorithm while the new entries determined are theunsupervised portion of the semi-supervised algorithm. In this manner, anon-exhaustive listing of drugs may be leveraged to train a MLA todetect drugs based on sentence structure, associated key terms, or otherpatterns in the text. Once trained, the unsupervised portion of thesemi-supervised algorithm will apply the training to detect unclassifiedwords for addition to the classification list. In this manner, asemi-supervised MLA can apply features of NLP to detect and classifyunknown and known drug entries in medical texts. While described hereinwith respect to the medical concept of a drug, this approach may beapplied to all medical concept classifications using the techniquesdescribed herein. Specific details of the NLP and MLA techniques arediscussed in more detail with respect to FIGS. 3 and 7-10, below.Specific details of supervised, semi-supervised, or unsupervised MLAtechniques are discussed in more detail below.

As discussed above, medical data may include numerous fields including,but not limited to, patient demographics, clinical diagnoses, treatmentsand outcomes, and genetic testing and laboratory information, and eachof the fields may also have a plurality of subfields. The above providedexamples, enumerations, and lists are not intended to limit the scope ofthe available fields and are intended to convey only the nature andstructure that fields within medical data may be represented within auniversal EMR. These fields of medical data may also identify conceptcandidates, discussed in more detail below with respect to FIGS. 3 and7-10. For example, Tylenol may be a concept candidate relating tomedication in treatment and outcomes.

Returning to FIG. 6, the sentence “The patient was given Tylenol 50 mgat 10:35 am.” in a document dated Jan. 1, 2001, may be encodedfield-by-field into the table 52 by identifying and populating one ormore fields of:

Text: The entirety of the text (“The patient was given Tylenol 50 mg at10:35 am.”).

Medication: Identifying any medication mentioned in the text (Tylenol).Medications may be brand name or generic name. This field does notinclude information about the dosage or method of administration.

Active Ingredient: Identifying the active ingredients (acetaminophen) ofthe medication mentioned using a list such as a search table linkingdrug names to their active ingredients.

Dosage & Dosage Units: The dosage (50 mg) associated with the medicationmentioned. In the above example, identifying that the dosage as 50 mg isfairly straightforward by reading the sentence, but clinical data isoften printed in tables with a variety of structures that are not easyto infer. As such, normalizing the dosage and dosage units by separatingvalue 50 into the dosage field and string “mg” or by selecting a knownvalue entry for the milligram units within a list may be preferable.

Document & Page: The document and page where the text is found (ProgressNote 01_01_01.pdf and page 3).

UMLS_CUI: The Concept Unique Identifier (CUI) field (C1234567) of theUMLS entry corresponding to the medication. The UMLS is a list ofmedical concepts (described in more detail with respect to FIG. 3,below) and the UMLS_CUI refers to the CUI field, which is UMLS'universal identifier. UMLS is comprised of a number of independentlymaintained clinical dictionaries and ontologies (such as those forcancer diagnosis & treatment, dentistry, veterinarian medicine, etc.).That is, the CUIs are universal to UMLS, such as there is only one CUIfor Tylenol across all of its constituent dictionaries that enables UMLSto unite all of these disparate sources.

UMLS_AUI: The Atom Unique Identifier (AUI) field (RXNORM#12345) is thedictionary-specific identifying code of the UMLS. Where the CUI isuniversal, and has the same entry across all included sources, the AUIfor Tylenol will have different AUIs for each dictionary that it has anentry in.

In one instance, the above fields, both the plurality of features 54 andtheir respective feature classifications 56 may be populated by a dataanalyst with sufficient medical knowledge and access to the requisitedatabases. Such an analyst may apply their education and experiences inthe field of medicine to identify any medications administered despiteconfounding factors present in the text (such as shorthand, typos,obscure references), their dosage, and understand the integration of thetwo in the provided text. However, analysts are constrained by theirhuman limits. Actions such as locating the data, opening it up in eithera physical or digital format, reading through documents of 100s or 1000sof pages, etc., all require considerable time. Furthermore, thecompanies and institutions which hire analysts must invest inconsiderable financial expenses to hire, train, and maintain teams ofanalysts. Incorporating a combination of machine learning algorithms(MLA) and natural language processing (NLP) algorithms into this processmay substantially improve the efficiency of the analysts or replace themaltogether. The MLA and NLP algorithms will be discussed in more detailswith respect to FIGS. 3 and 6-10, below. Before text may pass throughthe multiple layers of MLA and NLP algorithms, it must be extracted fromthe documents using optical character recognition (OCR) and cleaned upthrough a variety of pre-processing steps.

Returning now to FIG. 5, a high level overview of an exemplaryprocessing pipeline 60 is provided. An exemplary Intake Pipeline 62 maybe configured to perform the following processing steps: 1. OCR, 2.Pre-processing, 3. Sentence Splitting, 4. Candidate Extraction, 5.Entity Linking, 6. Entity Normalization, and 7. Entity Structuring.Specifically, and with reference to FIG. 5, pipeline stage 64 forpre-processing may include OCR and text cleaning, stage 66 for parsingmay include NLP algorithms for sentence splitting and candidateextraction, stage 68 for dictionary lookups may include entity linking,stage 70 for normalization may include entity normalization, stage 72for structuring may include entity structuring, and stage 74 forpost-processing may include structuring the data and formatting it intoa universal EMR or institution based EMR format. Due to the asynchronousand modular nature of the pipeline stages, each stage may pass datadirectly to the next stage based on processing availability or may storedata in a corresponding portion of a storage component or database. Inan exemplary embodiment, a sentence splitting algorithm may be stored ina cloud based server or on a local/remote server 76 and may beincorporated into the parser at stage 66, a fuzzy matching algorithm 78may be incorporated into the dictionary lookup at stage 68 and anOntological graphing algorithm 80 may be incorporated into thenormalization at stage 70.

For example, upon receiving a record update or a request in the form ofa clinical document, a database of multiple documents, or another formof patient record, the request may pass through a pre-processingsubroutine 82, a parsing subroutine 84, a dictionary lookup subroutine86, a normalization subroutine 88, a structuring subroutine 90 forfiltering and/or ranking, and a post-processing subroutine 92 in orderto generate and serve a response to a remainder of the system. The firstfour of these subroutines may encompass a first layer, in which thesystem identifies and structures clinical concepts with correspondingmetadata (clinical or medical concepts) extracted from clinicaldocuments.

The intake pipeline 62 receives a clinical document that may includemachine readable text or that may be received as an image file. Ifnecessary, the document may be submitted to a pre-processor stage 64that performs text cleaning and error detection (format conversion,resolution conversion, batch sizing, text cleaning, etc.). Oncepre-processed, the document may be submitted for OCR on the document toconvert the text into a machine-readable format (text document, html,etc.). Once in a machine-readable format, the error correction (such asspell checking, noise removal, context based correlation, etc.) may beperformed on the now-machine-readable text. The intake pipeline stages64-70 are modular components, which allows for real-time selection ofthe best processing tools and software depending on the type of documentand document content being processed, enabling the processing pipelineto replace/compare algorithms used as necessary. Two examples of OCRsoftware that may be used include Tesseract and Google Cloud Vision API.Tesseract provides high-speed OCR for documents which do not have anyartifacting/noise (documents that have been printed to PDF or that hadvery little noise generated during the scanning process). Google CloudVision API, conversely, may be used for documents which have too muchnoise, as it is well-suited to process old documents or images ofdocuments that have been scanned/faxed many times, introducing extensiveartifacting and noise into the image. As a result, Cloud Vision mayprovide detailed information about the position of paragraphs, words,and documents within the documents processed. Other OCR systems may alsobe utilized in lieu of or in combination with the two described above.

The modularity of each processing stage requires differentpre-processing mechanisms for each OCR service/software implemented. Forexample, different OCR services support some image formats andresolutions for OCR but may not support others. When processing patientrecords, many document formats included within the record areunsupported, and may require format conversion from the unsupportedformat to a supported format, as well as additional processing forparameter optimization for each respective document to achieve the bestresults from the OCR service selected, as discussed above. For example,when utilizing Google Cloud Vision, images may need to beformat-converted to 300 dpi JPG files. Furthermore, Google Cloud VisionAPI charges for OCR on a per-request basis, but supports requests of upto 4 MB and supports batch requests (as many images as can be fit intoone 4 MB request) for no extra cost. Additional processing may beperformed to include additional document images into a request to placeeach request at the maximum file size and use batch processing todecrease costs.

Documents received at the pre-preprocessing stage may be in various textformats (such as DOC, DOCX, RTF, or as values in aspreadsheet/database). For simple documents, pre-processing may beperformed by simply extracting any text directly (such as TXT, RTF,etc.), but some require advanced software to parse the file formats(such as DOCX, PDF, ACCDB). Exemplary software for parsing more complexfile formats include pandoc and PDFBox.

As with the OCR steps discussed above, in another embodiment, additionalpre-processing may be performed after submitting an image to OCR todetermine whether the detected text is “reasonable” before outputtingfinal results. While some OCR technologies may perform their ownreasonability determination, it may be necessary to further improve uponthe quality of the OCR output by performing a text cleaning algorithm onthe OCR output. Text cleaning may be implemented by a category of NLPmodels designed for Language Modeling. Additionally, machine learningalgorithms and deep learning algorithms may be utilized to furtherimprove upon the OCR results. Exemplary categories of language modelsmay include: statistical (n-gram), graphical (CRF/HMM), and neural (RNN,LSTM, skipgram, BOW, etc.). While each category of language model mayprocess datasets of particular structure and content differently, themodular nature of the processing pipeline allows the most appropriatelanguage model to be selected based upon the document being processed.For instance, a first language model may be selected if the document isa progress note while a second language model may be selected if thedocument is a lab result. As another example, a first language model maybe selected if the document is from a first institution and a secondlanguage model may be selected if the document is from a secondinstitution. As another example, a first language model may be selectedif the document is from a first clinician and a second language modelmay be selected if the document is from a second clinician.

In one aspect, due to the frequency of tables, charts, structuredheaders, and other features in medical documents, neural language modelsmay be preferred. Neural networks for language modeling may be trainedover millions of sentences and perform best when trained over text fromthe same domain as they will encounter in a production system. Forexample, language models trained over medical/clinical text will performbetter in medical-based OCR text cleaning tasks than language modelstrained over online reviews, news articles, or other generic andfreely-available sources. Similarly, language models trained overclinical documents that are specific to a particular disease state, suchas cancer, may perform better in medical-based OCR text cleaning tasksupon disease state-related clinical documents than language modelstrained over clinical documents that are not specific to a particulardisease state. By providing a training set having millions of clinicaldocuments that are similar to the documents submitted for OCR, anexemplary language model may be trained over in-domain text that manytraditional NLP sources do not have access to, resulting in a morerobust language model.

Language models may estimate the probability of a given sequence ofwords or characters (letters, numbers, punctuation, etc.) occurring in acurrent document based on the frequency of the given sequence of wordsor characters as they appeared in the original training documents.Language models may identify regions of OCR output that are uncommon inthe training text (such as “stage iv beast cancer” is an unlikelysequence of words in medical documents). Language models may alsoidentify which words/characters were most likely to have occurred ineach position in text, for example, “stage iv ______ cancer” may have ahigh probability for “lung” and “breast” filling the blank. By combininga probability distribution over words most likely to fill the blank(such as in this example cancer sites, but may be medications, dates,diagnosis, treatment results, etc.) and words most likely to be OCR as“beast,” the system may determine that “beast” was most likely “breast”without having to look at the image itself and only relying onlinguistic patterns.

A probability distribution may be generated by applying a neural networkfor Named Entity Recognition (NER). For example, individual words may beprovided a weighting factor for probability of occurrence across amassive training set. Statistical information may be stored thatindicate likely phrases, based off a starting word, and any followingwords of a phrase. Each word, in turn, may be applied a weight aboutwhether it is a starting word or a following word and the likelihoodthat the word is part of a phrase or standing alone in the text.

In one example, the phrase “stage iv ______ cancer” may be processed.“Stage” may be provided a starting word score of 0.6, a following wordscore of 0.3, and a standalone score of 0.1 which would account for theentirety of the potential distribution of the word's appearance in thetraining text. The word “iv” may be provided a starting word score of.05, a following score of 0.55, and a standalone score of 0.4. The word“cancer” may be given a starting score of 0.1, a following score of 0.7,and a standalone score of 0.2. A sentence analysis for the exemplary NERmay find that because “stage” has a high probability for being astarting word and “iv” has a high probability for being a followingword, that “______” may have a higher probability for being a followingword that matches “stage iv ______” or “stage iv ______ cancer” in aphrase.

Additionally, because “cancer” similarly has a high probability forbeing a following word, NER may predict that the “______” is either afollowing word that continues the word beginning at “stage” or may be abeginning word that begins before “cancer”. Because the word “beast” hasa beginning word score of 0.1, a following score of 0.2 and a standalonescore of 0.7, the model may flag that “beast” does not fit within theexpected sequence of words. By comparing similar words, (such as breast,feast, rest, roast, wrest, etc.) the NER model may identify that breasthas a beginning score of 0.5, a following score of 0.3, and a standalonescore of 0.2, making breast fit within two models of the predictedphrases and selecting “breast” to replace “beast” based on the predictedphases alone. The modified phrase then may be further tested, or testedalone using a more generalized probability distribution. For example,the training date may weight the occurrence of words in medical texts.As discussed above, while the word “beast” may rarely occur in a patientreport, (such as patient was mauled by unknown beast), “breast” mayoccur more frequently (such as patient expresses concern re: lump inbreast, breast cancer, stage iv breast cancer, patient's breastrecovered from surgery, etc.), giving “breast” a much higher probabilityof occurrence weighting than “beast,” such similarity analysis likewisecan apply to an EMR/ERR. As a result, the preprocessing stage 64 mayreplace “beast” with “breast,” terminate pre-processing, and indicatethat the resulting text is reasonable.

In an alternate embodiment, a tabular extraction method may be performedacross EMR and EHR documents, similar to the tabular extraction methoddiscussed above with regard to the output of the electronic documentcapture, such as incorporating the exemplary tabular extraction approachinvolving masks 1-3 of FIG. 4. Tabular extraction involves applying MLAand deep learning algorithms to optimize the OCR process for reportswhich may have a standardized format.

Returning to FIG. 5, once the pre-processing stage 64 has completed, thegenerated OCR output may be stored for later retrieval by the parserstage 66 of the intake pipeline 62. In an alternative embodiment, thepreprocessing stage may check in with parser 66 to confirm availabilityand pass the OCR output to the parser stage directly. Due to the modularnature of the intake pipeline 62, each processing stage may processtheir respective data without regard for the specific OCR orpre-processing methods. A modular pipeline approach allows the pipelineto swap in and out the most appropriate OCR and pre-processingtechnologies to improve the results of the overall processing.

Sentence splitting is a function of NLP that may be incorporated toparse sentences into meaningful structures. Documents may arrive ineither plaintext format (containing all text from the document) or in astructured OCR format (including the text as well as bounding boxes forevery character, word, and sometimes paragraph if the model is capableof identifying paragraph regions). Conventional sentence splitting maybe implemented by many readily available NLP applications, including,such as any of CoreNLP, Spacy, AllenNLP, or NLTK. The system mayimplement a plurality of NLP applications, and identifying a mostappropriate tool for sentence splitting may be depend on the nature ofthe clinical documents at hand, since clinical documents have a largevariety in document layouts and content. Each tool for sentencesplitting has advantages for particular types of documents, expectedsentence structures, etc. In particular, documents often have headersand footers with useful structured text data, but headers/footers maynot be presented in a standard sentence format (such as documentcitation or quote) and may confound certain sentence splitters.Similarly, doctors may use clinical shorthand which conventional NLPtools are not trained to parse; for example, a doctor may write “pt dxluad 2017” to mean “the patient was diagnosed with lung adenocarcinomain 2017.”

These deficiencies in sentence splitting may be overcome by addingmodels before this stage to identify whether text is semi-structureddata, well-formed text, clinical shorthand, uninformativeheaders/footers, etc. By creating methods for distinguishing betweenthese types of text, the intake pipeline may use specific models toextract information from each type. For example, complex sentences maybe broken down into simple sentences by looking for coordinationconstructs, adjectival clauses, evaluating parataxis, prepositionalphrases, etc., by applying phrase-based or syntax-based machinetranslation approaches. For sentences which are well-structured (such asfollowing traditional grammar and prose), parse trees or deep semanticrepresentations may be utilized. For sentences which are noisy (such asstructured, but with unclear boundaries), a maximum entropy approach maybe utilized. In texts which are very specialized in nature (such asmedical texts, legal texts, etc.), a tokenization and documentsegmentation algorithm may be applied. By implementing sentencesplitting, the processing pipeline may split the document into sentencesfor individual parsing.

Candidate extraction may be performed using one of above-referencedapproaches. For example, one approach may include a symbolic approachthat relies on the structure of the sentence. Relying on the structuremeans that the sentence may be passed into a dependency parser orconstituency parser.

Constituency-based parse tree text analysis systems may incorporate alist of phrase types that are likely to occur in sentences containingmedical concepts. A subset of phrase types from the improved list ofconcepts may include:

CC—Coordinating conjunction, (such as and, but);

CD—Cardinal number, (such as one, two, 1, 2);

DT—Determiner, (such as a, the);

EX—Existential clause, (such as there);

*FW—Foreign word, (such as absentia, nauseam, habeas);

IN—Preposition or subordinating conjunction, (such as although,because);

*JJ—Adjective, (such as wet, fast);

*JJR—Adjective, comparative, (such as -er);

*JJS—Adjective, superlative, (such as -est);

LS—List item marker, (such as numbering, bullets);

MD—Modal, (such as shall, will, might);

*NN—Noun, singular or mass, (such as cell, cancer);

*NNS—Noun, plural, (such as cells, fingers);

*NNP—Proper noun, singular, (such as California, London);

*NNPS—Proper noun, plural, (such as the Joneses, the Bushes);

PDT—Predeterminer, (such as both, a lot);

POS—Possessive ending, (such as 's);

PRP—Personal pronoun, (such as we, she);

PRP$—Possessive pronoun, (such as his, hers);

*RB—Adverb, (such as quite, then);

*RP—Particle, (such as not, to);

*SYM—Symbol, (such as @, &);

*UH—Interjection, (such as ah, oh);

*VB—Verb, base form, (such as run, inject);

*VBD—Verb, past tense, (such as ran, injected);

*VBZ—Verb, 3rd person singular present, (such as runs, injects);

WDT—Interrogative determiner, (such as what, which);

WP—Interrogative pronoun, (such as who, whom);

WP$—Possessive interrogative pronoun, (such as whose);

WRB—Interrogative adverb, (such as where, how); and

.—Period character.

While conventional implementations are not optimized for technical texts(medical texts), the conventional list of phrase types may be augmentedto include additional phrase types to optimize sentence splitting formedical-based texts. Such additions have been indicated with an asterisk(*). Conventional implementations that involve constituency-based parsetrees include Apache cTAKES™, Stanford Parser, TensorFlow, andCharniak-Johnson.

Turning to FIG. 7, one example of a constituency-based parse tree isdepicted. In that example, a constituency-based parse tree may receive asentence “the patient was given tylenol 50 mg at 11:35 am.” from which aparse tree may be generated. As depicted in the tree of FIG. 7, conceptsmay be identified (such as medical concepts) using different linguisticphrases and parts of speech. An example constituency parser then maygenerate: (ROOT (S (NP (DT The) (NN patient)) (VP (VBD was) (VP (VBNgiven) (NP (NP (NNP Tylenol) (CD 50 mg)) (PP (IN at) (NP (CD 11:35am)))))) (. .))).

In this example, phrase types: S, VP, NP, and PP markers are not in theabove list. They represent the top-level sentence, verb phrase, nounphrase, and prepositional phrase, respectively. Furthermore, “patient”,“Tylenol”, “Tylenol 50 mg”, “50 mg”, and “11:35 am” may be included in alist of concept candidates 96 (graphically represented as dotted linesaround the words in the parse tree). Concept candidates may bedetermined by noting important phrase types (such as NP, CD, etc.) andmay be further refined by comparing any associated text against a listof weighted words, whereby words which are weighted above a thresholdweight may be presented as concept candidates. For example, the word“patient” may be flagged as a concept candidate, but due to its lowweighting factor, may be removed from the candidate list.

In another embodiment, an MLA may be utilized to identify conceptcandidates. An exemplary MLA for identifying concept candidates includesa name entity recognition (NER) model. NERs may be implemented usingconditional random fields, convolutional neural networks, attentionbased neural networks, long short term memory networks, or other neuralmodels.

Language models may vary based upon the type of document beingprocessed, (such as pathology reports, progress notes, and other EHR andEMR documents, etc.), to optimize the type of information which may beextracted from the documents. For example, a whole document classifiermay be applied to a progress note (physician generated report of patientstatus on each checkup), pathology report, or other EHR/EMR documents toidentify a patient's gender, cancer types, or other information that mayrequire verification over one or more documents to provide reliablepredictions. For a whole document classification, the text of the entiredocument may be evaluated before the document as a whole is classified(such as male/female, lung/breast cancer, date of birth, etc.). Forother types of information, a sequence labeling classifier may beapplied to a progress note, pathology report, or EMR/EHR documents toidentify, for example, medications taken by a patient, therapies apatient may be undergoing, or other information which may be difficultto extract due to the extensive number of varying entries for each typeof class. For a sequence labeling classification, each sentence, orcombination of sentences in the document may be evaluated before thedocument is assigned another classification for identifying a classentry (such as a medication or therapy of the patient). Theimplementation details of an exemplary whole document classifier andsequence labeling classifier are discussed below.

In one aspect, a whole document classifier may rely on a training modelthat has been trained on thousands of medical documents found in EMRsand EHRs of patients. The training data may be provisioned with theparts of speech assigned to words and the true classification for eachpatient (such as male/female, age, ethnicity, etc.). A machine learningalgorithm or a neural network may process the training data to generatea rule set or a trained neural network, respectively. In an exemplaryrule set, a list of words with corresponding weights may be generatedbased upon the frequency they appear in text with proper classificationvs text without the proper classification. For example, a rule set fordetermining if a document for a patient is to be classified according togender may have a list of words including “male”, “man”, “he”, “his”,“testicular”, “prostate”, etc., which are weighted heavily towardsidentifying gender as male and a list of words including “female”,“woman, “her”, “she”, “breast”, “ovaries”, “ovulation”, “menstrual”,etc., which are weighted heavily towards identifying gender as female.

The rule sets may include a vector of, for example, three hundred wordsand their respective weights, and each rule set may be applied over allwords in a sentence to generate weights for every sentence. For example,a sentence “The patient was given prostate exam after he complainedabout having difficulty urinating in the mornings” may be given a highweight for gender as male because of words “prostate exam” and “he”.After each word of each sentence is processed, each respective sentencemay be assigned a sentence vector (such as 10% female, 90% male), theneach sentence in a document may be processed to assign a documentvector, and finally, each document in a patient's EMR or EHR may beprocessed to assign a patient vector.

At each level of granularity, the whole document classifier may beinterrupted, for example, if a sufficient level of certainty has beenreached or processing was intended to terminate at that level. Forexample, if a document has been determined to have a high incidence ofaccuracy because a table on page 3 of a document may always return thecorrect gender for the patient, then the algorithm may identify thathigh accuracy has been provided for the document based on the onesentence of that document and stop processing a gender classification atthe sentence level vector for that patient. Furthermore, a patient levelvector may not be generated if a document level vector has reached acertain threshold of certainty (such as 95%), or if, for example, onlyone document is being processed.

FIG. 8 provides a visual representation of word weightings for asentence 98 containing “The patient was given Tylenol 50 mg at 11:35am.” At the word level, “the”, “was”, “given”, and “at”, may be givenlow weights, “patient” and “11:35 am” may be given medium weights, and“Tylenol” and “50 mg” may be given high weights. As a result, theoverall sentence may be classified with a high weight 100 (such as 95%)that medication the patient has taken includes Tylenol 50 mg. For thisexample, because such a high confidence value is determined, theprocessing may not need to continue to evaluate other sentences in thedocument to determine that the patient did indeed take Tylenol 50 mg,but each sentence 102, 104 will be processed to determine if otherconcepts are identified (such as to identify gender, other medications,other treatments, or demographic information). In this example, eventhough only the medication concept is given a high weight, each of theidentified concept candidates may be retained for the next stage of theintake pipeline for further processing; alternatively, those identifiedconcept candidates may be dropped from the candidate list.

In some circumstances, a high level of confidence may not be available.For example, a patient who has undergone a gender reassignment surgerymay have documents with a high level of confidence for one gender beforesurgery and a high confidence for another gender after surgery, or adocument for a patient of a different gender may have been misfiled inthe current patient's file. When a level of certainty lies below athreshold value (such as 90%), the whole document classifier may outputthe highest level vector calculated identifying, for example, a 60%confidence male and 40% confidence female. The output may also includeone or more identifiers for which document, which section of whichdocument, which sentence, or even which word from which the confidencevalues were calculated. In another embodiment, no prediction may begenerated when the confidence value is below the threshold. In stillother embodiments, documents which have contention in a prediction maybe flagged, a true determination of classification may be obtained, andthe documents and the true classification may be provided to a trainingengine which may retrain the rule set or neural network to furtherimprove accuracy.

As discussed above, in another aspect, a sequence labeling classifiermay be implemented. An MLA or neural network may be trained to generatea rule set identifying words and word sequences which are likely toidentify concept candidates. Such concept candidates may includestand-alone words such as “patient,” “age,” or “gender,” with a highstand-alone rating. It should be noted that these words may not becommonly coupled with other words in medical text but may still havesome word couplings (such as under age). Other concept candidates mayinclude words which are commonly linked to other words in a medicaltext. Words which commonly begin a multi-word concept include “breast”(such as breast cancer, breast reduction, breast augmentation, breastsurgery) and “stage” (such as stage I cancer, stage II cancer, etc.).Other such words may include “high” (such as high blood pressure), “low”(such as low cholesterol), or “heart” (such as heart attack, heartfailure). Words which commonly begin a multi-word phrase may feature ahigh beginning score and a medium stand-alone score. Intermediary wordsin a multi-word phrase (such as ______ cancer, ______ cell, ______failure) are words which may have a high intermediary score and a mediumstand-alone score). For example, each word in a sentence may be assigneda value for the likelihood that the word is a beginning of a multi-wordphrase (such as a “B” value), an intermediary of a multi-word phrase(such as an “I” value), and a standalone word (such as an “O” value),and then each word or collection of words may be evaluated to identifyclinical concepts.

Turning to FIG. 9, a sequence labeling classifier 106 may provide a“BIO” score for each word, where a BIO score (10, 30, 60) would meanthat the associated word is the first word in a multi-word phrase inabout 10% of its occurrences in the training set, an intermediary wordin a multi-word phrase in about 30% of its occurrences in the trainingset, and a stand-alone word in about 60% of its occurrences in thetraining set. For example, the word “the” almost always precedes anotherword and occasionally is an intermediary word of a multi-word phrase, somay be provided a BIO score 108 of (90, 10, 0). “The” may also beconsidered an extraneous word, despite almost always preceding otherwords of importance, so it may be provided a BIO score of (0, 10, 90) toprevent processing, “patient” may be provided a BIO score 110 of (5, 20,75), and “was” may be provided a BIO score 112 of (0, 0, 100). Thesequence labeling model may begin processing the sentence at the firstword, “the,” and then note a high incidence of that word being thebeginning value of a multi-word phrase (in the first incidence where BIOscore is (90, 10, 0)), process the second word “patient” to note a highincidence of being an intermediary or stand-alone word, and process thethird word “was” to note a high incidence of being a stand-alone word.By recognizing a potential beginning of a multi-word concept, apotential intermediary of a multi-word concept, and a distinctnon-multi-word entry, the sequence labeling model may identify a firstmulti-word concept. Therefore the sequence labeling model may indicate“the patient” 114 as a likely candidate concept for the multi-word labeland “patient” 116 as a likely candidate concept for the stand-alone wordlabel.

Processing may continue word-by-word until another stand-alone word (B,I, or O labels) or multi-word (BIII . . . labels) are detected. In theexample of FIG. 9, another multi-word phrase 118 may be detected at“Tylenol 50 mg,” and concepts “Tylenol” and “Tylenol 50 mg” may begenerated. A final concept 120 may be generated at “11:35 am.”

A sequence labeling classifier may be able to identify labels with ahigher accuracy than a parse tree by linking words together throughtheir labels (such as BI, BII, BIII, etc.) to identify multi-wordconcepts (such as heart attack, stage IV cancer, medial tibial stresssyndrome, etc.) as the totality of their concept rather than each of thewords in multi-word concept.

The number of candidate concepts which may be extracted may beneedlessly large. For example, in patient file with thousands ofdocuments, a concept candidate for breast cancer may occur hundreds oftimes, a concept for lung cancer may occur tens of times, and a conceptfor liver cancer may only occur once. It may be useful to filter/rankthe mentions of each concept candidate to reduce repetition in thefollowing stages in the pipeline. For concept candidates which may beconsolidated (such as mentions of breast cancer for diagnosis) theconcept candidate may be reduced to a single concept with a count fieldin the hundreds. Furthermore, if concept candidates are competing forthe same field, the concept candidate may be coupled with a reliabilityindex based upon the frequency of the concept candidate occurring inrelationship to the others (such as 200 mentions of breast cancer, 13mentions of lung cancer, and 1 mention of liver cancer may be processedto a 200/214 reliability index that the patient has breast cancer). Thehighest ranked competing concept candidate may be preserved along with areliability index, or a consolidated report of the most frequentcompeting concept candidates may be preserved along with their countvalues and/or reliability index.

Using any of the above methods, candidate extraction generates aplurality of candidate concepts which may be evaluated in the followingstage for entity linking.

Returning to FIG. 5, the entity linking pipeline stage 68receives/retrieves the candidate phrases as a list and may process eachcandidate to identify any links between the phrases and known entities(such as the enumerated list of medical drugs discussed above). Entitylinking is the task of determining whether a candidate concept (phrase)is a relevant clinical concept. Relevancy may be determined by thepresence of the candidate concept in any medical dictionary or theuniversal dictionary described above. Relevancy may also be determinedbased on proximity to a concept candidate hit. For example, a time“11:35 am” may not result in a hit in any dictionary as a medicalconcept. However, certain medical concepts, such as medications, mayfall within an abstraction category such as treatment. A treatment mayhave fields such as treatment type (the medicine) and date and time oftreatment (11:35 am). By considering proximity to other conceptcandidates, key information may be retained even if the concept may notexist in the database. The retained candidate concept may not beclassified as a linked entity, but may be associated with the linkedentity for abstraction purposes.

Within the entity linking pipeline stage 68, the list of conceptcandidates generated in the previous pipeline stage may be provided to adictionary lookup for matches. Conventional dictionary lookup tools mayinclude Elasticsearch, Solr, Algolia, or Sphinx. In one aspect, a directdictionary lookup may not always result in a database hit (the candidateis in the database) because of typographical errors, OCR errors,shorthand, or other confounding factors. In those situations, candidateswhich are not an exact match may still be found in the database byapplying fuzzy matching logic. For example, the entity linking pipelinestage 68 may expect to find matches for “Tylnol” and “Tylnol 50 mg”because exemplary queries allow for “fuzzy matching,” which will correctpotential typographical errors or OCR errors that occur in “Tylenol.”

Fuzzy matching may be implemented by an approximate string matchingalgorithm, such as the exemplary fuzzy matching algorithm discussedabove.

Fuzzy matching is structured around the text concepts included in theabove enumerated list or the UMLS, including metadata fields CUI (theUMLS unique ID) and AUI (dictionary-specific unique ID), so that anexhaustive search may be performed for all medical concepts. Thedictionary search engine may also return metadata about the specificentry detected (such as universal ID assigned in the above enumeratedlist or the UMLS), which is useful for understanding Tylenol as amedical concept and not just the correct spelling of a drug. At the endof text normalization, some of the extracted candidates may have zeromatches but others may have many matches. For example, there are manyversions of Tylenol throughout the UMLS database because of the numberof dictionaries represented therein. Fortunately, the CUI (the UMLSuuid) provides a generalization to join similar concepts, which reducesthe number of matches from one for each potential database to the numberof unique CUIs represented. Not all concepts can be simplified sosuccinctly, though. For example, “Tylenol” is a different concept than“Tylenol 50 mg”, which is a dosage-specific version of “Tylenol”. Anyambiguation from “Tylenol 50 mg” to “Tylenol” would effectivelyconstitute a loss of information.

As discussed above, fuzzy matching may also apply on a word-by-wordbasis rather than a letter-by-letter basis. Furthermore, in stillanother embodiment, both fuzzy matching on a character by characterbasis and word by word basis may be applied concurrently to generateentity matches.

Certain features, such as the TNM Classification of Malignant Tumors(TNM) is a globally recognized standard for classifying the extent ofspread of cancer, must be preempted from fuzzy matching. TNM is anotation system that describes the stage of a cancer, which originatesfrom a solid tumor, using alphanumeric codes: T describes the size ofthe original (primary) tumor and whether it has invaded nearby tissue; Ndescribes nearby (regional) lymph nodes that are involved; and Mdescribes distant metastasis (spread of cancer from one part of the bodyto another). For example, T may be designated a value to estimate sizeor direct extent of the primary tumor (Tx: tumor cannot be assessed,Tis: carcinoma in situ, T0: no evidence of tumor, T1, T2, T3, T4: sizeand/or extension of the primary tumor), N may be designated based uponthe degree of spread to regional lymph nodes (Nx: lymph nodes cannot beassessed, N0: no regional lymph nodes metastasis, N1: regional lymphnode metastasis present; at some sites, tumor spread to closest or smallnumber of regional lymph nodes, N2: tumor spread to an extent between N1and N3 (N2 is not used at all sites), N3: tumor spread to more distantor numerous regional lymph nodes (N3 is not used at all sites), and Mmay be designated based upon the presence of distant metastasis (M0: nodistant metastasis, M1: metastasis to distant organs (beyond regionallymph nodes)). Exemplary TNM codes may be “pT1 pN0 M0” or “pT4 pN2 M1”.Due to the importance of the TNM codes being parsed precisely as theyappear to maintain the TNM values, fuzzy matching may be disabled forstop words relating to TNM values, for example, “t0”, “T1a”, “t3”, sothat fuzzy matching does not change a “t1” into a “t2” to match adatabase Entity. NLP may be combined with restricted fuzzy matching incertain embodiments to correct OCR errors related to TNM codes. Forexample, a NLP model may detect that TNM is being referenced bydetecting the presence of a T, N, and M code; however, classificationmay fail due to an OCR of “pT0” with “pTo”, by allowing a restrictedfuzzy matching of only similar characters (such as an “o” for an “0”),TNM codes may be maintained while still correcting for errors.

Due to the large volume of concept candidates that may exist from theprevious pipeline stage, merely searching for a match and terminatingthe search upon finding a single match may provide a substantial benefitin reducing the processing time spent crawling the relevantdatabases/dictionaries. However, the best matches may not be the firstmatches, and if there are multiple matches within a group (such assynonyms which are off by a single word to the concept candidate), itmay be necessary to pick the match which has the lowest fuzzy “score”(the value that counts the number of errors corrected to generate thefuzzy match). If there are still ties (such as there are two matches ofequal fuzzy “score”), then the tied matches may be sorted based onlength of characters or length of words (such as shorter matches withless words/characters score higher than longer matches with morewords/characters). Any unresolved matches may then be selected randomlyor according to a first-in, first-out FIFO queue of matches, such thatthe first match is selected.

Templates, Fuzzy Text Matching & Regular Expressions:

Many reports within EMRs and EHR are provided in consistent formattingacross institutions for periods of time (such as patient intakes mayshare the same form for a period of time until the next revision).Relying on this consistency, the system may consider a case where ahospital system prints its pathology reports using the same template andhad a different template for any documents that were created before Jan.1, 2001. If Pathology Reports from this hospital system are identifiedas frequent documents received in EMR and EHR, optimizations may beapplied to processing to create methods for extracting information fromknown locations within the shared templates of each respective form. Anexemplary method (such as the method described above) may also includemultiple parts, as follows:

Document classification: The system may generate an image or textclassification model to: determine whether a given document belongs toone of the templates that may be extracted from, assign the document anidentifier for linking the document to the template, use the identifierto look up the classification model optimized for the document, andclassify the document. Exemplary template-based approaches and tabularapproaches are discussed above.

Regular Expressions: The system may identify anchor strings regularlyoccurring in text that identify where key health information may reside.For example, the system may recognize that “DOB” is a string to searchfor dates of birth and “Pathological Diagnosis” may be a header to asection that provides concepts for linking to a pathological diagnosis.

Fuzzy Text Matching: As discussed above, the system may apply a fuzzysearch algorithm to a regular expression in order to allow theapplication of regular expressions to words which have OCR errors,typographical errors, or are otherwise confounded.

Templates: Once a document has been classified, and regions of text maybe determined in advance, an image classification model may leverage thepredetermined region locations to identify those same regions within adocument image to extract key health information (clinical concepts).For example, document headers may often be visually structured forpresenting information to the reader, and that known visual structuringmay contain useful demographic information. By identifying a documentheader, processing may include rotating/skewing the image to line up thetemplate, removing image irregularities, OCR of the text, and applyingregular expressions to extract any information from the standardizedformat. Any concepts extracted from the template may be provided to theentity linking pipeline 140 and may be processed to identify anyrespective matching concepts for linking.

Returning to FIG. 5, in another embodiment, entity normalization (suchas at step 70) may be applied to determine which of the entity linkedconcepts of the previous stage are relevant to abstraction and, if theyare relevant, which encoding schema may be applied to encapsulate theabstraction completely. For example, “Tylenol” and “Tylenol 50 mg” maymatch in the dictionary from UMLS with a concept for “acetaminophen”. Itmay be necessary to explore the relationships between the identifiedconcept from the UMLS dictionary and any other concepts of relateddictionaries or the above universal dictionary. Though visualization isnot required, these relationships may be visualized through agraph-based logic for following links between concepts that eachspecific integrated dictionary may provide.

FIG. 10 is an exemplary ontological graph database 122 for viewing linksbetween different dictionaries (databases of concepts) that may beinterlinked through a universal dictionary lookup in order to carry outthe normalizing stage 70 in FIG. 5. Conventional ontological graphdatabases may include GraphT, Neo4j, ArangoDB, Orient, Titan, orFlockdb. The following references to dictionaries and databases are forillustrative purposes only and may not reflect accurately theconcepts/synonyms, entities, or links represented therein. Links betweentwo concepts may represent specific known relationships between thosetwo concepts. For example, “Tylenol” may be linked to “acetaminophen” bya “trade name” marker, and may be linked to “Tylenol 50 mg” by a “dosageof” marker. There may also be markers to identify taxonomic “is a”relationships between concepts. “Is a” markers provide relationshipsbetween over some clinical dictionaries (such as SNOMEDCT_US, Campbell WS, Pederson J, etc.) to establish relationships between each databasewith the others. For example, we can follow “is a” relationships from“Tylenol”, “Tylenol 50 mg”, or “acetaminophen” to the concept for ageneric drug. Such a relationship may not be available for anotherconcept, for example, a match to the dictionary for UMLS to “thepatient” or “patient” may not have a relationship to a medicationdictionary due to the conceptually distinct natures of each entity.Relationships may be found between drugs that have the same ingredientsor are used to treat the same illnesses.

Other relationships between concepts may also be represented. Forexample, treatments in a treatment dictionary may be related to othertreatments of a separate treatment database through relationshipsdescribing the drugs administered or the illness treated. Entities (suchas MMSL#3826, C0711228, RXNORM# . . . , etc.) are each linked to theirrespective synonyms, (such as Tylenol 50 mg, Acetaminophen, Mapap,Ofirmev, etc.). Links between concepts (synonyms), may be explored toeffectively normalize any matched candidate concept to an RXNORM entity.

Returning to FIG. 10, the concept candidate “Tylenol 50 mg” 124 may havea hit in the National Library of Medicine Database MMSL. In thepreceding stage of the pipeline, “Tylenol 50 mg” may have been linked tothe Entity MMSL#3826 126 as an identifier for the “Tylenol 50 mg”concept in MMSL. The linked Entity, MMSL#3826, may reside in a databasewhich is not a defined database of authority, or, for documentclassification purposes, MMSL#3826 may not provide a requisite degree ofcertainty or provide a substantial reference point needed fordocument/patient classification. Through entity normalization, it may benecessary to explore links to MMSL#3826 until a reference entity ofsufficient quality is identified. For example, the RXNORM database maybe the preferred authority for identifying a prescription whenclassifying prescriptions a patient has taken because it provides themost specific references to drugs which are approved by the U.S. Foodand Drug Administration (FDA).

Other authorities may be selected as the normalization authority basedupon any number of criteria. The exact string/phrase “Tylenol 50 mg” maynot have a concept/entity match to the RXNORM database and the appliedfuzzy matching may not generate a match with a high degree of certainty.By exploring the links from MMSL#3826, it may be that concept “TylenolCaplet Extra Strength, 50 mg” 128 is a synonym to “Tylenol 50 mg” in theMMSL database. Furthermore, concept “Tylenol Caplet Extra Strength, 50mg” may also be linked to Entity C0711228 130 of the UMLS database. Byexploring the synonyms to “Tylenol 50 mg” 124 through Entity MMSL#3826126, the concept candidate may be linked to the UMLS Entity C0711228130. However, the UMLS Entity C0711228 130 is not the preferredauthority for linking prescriptions, so further normalization steps maybe taken to link to the RXNORM database. Entity C0711228 130 may havesynonym “Tylenol 50 MG Oral Tablet” 132 which is also linked toRXNORM#5627 134. RXNORM#5627 134 may be a normalization endpoint (onceRXNORM#5627 has been identified, normalization may conclude); however,RXNORM#5627 134 may also represent the Tylenol specific brand namerather than the generic drug name. A degree of specificity may be placedfor each source of authority (normalization authority) identifyingcriteria which may been desired for any normalized entity. For example,a medication may need to provide both a brand drug name and a genericdrug name. Links in the RXNORM database may be explored to identify theEntity for the generic drug version of Tylenol. For example, RXNORM#5627134 may have an “ingredient of” link to RXNORM#2378 136 which has a “hastradename” link to RXNORM#4459 138 with concept acetaminophen.RXNORM#4459 138 is the Entity within the RXNORM database whichrepresents the generic drug 140 for Tylenol 50 mg and is selected as thenormalized Entity for identifying a prescription in the classificationof prescriptions a patient has taken. In this aspect, normalization mayfirst identify an Entity in the dictionary of authority (as definedabove) and may further normalize within the dictionary of authority to adegree of specificity before concluding normalization.

For each field of medical data that is abstracted in the intakepipeline, reasonable reference points for normalization may beidentified (such as RXNORM for medications, SnoMed for cancers) andwhich types of relational links may be traversed from matched conceptsin the fields of medical data. As described above, medical data mayinclude fields of patient demographics (such as patient name, date ofbirth, gender, ethnicity, date of death, address, smoking status,diagnosis dates, personal medical history, family medical history,etc.), clinical diagnoses (such as date of initial diagnosis, date ofmetastatic diagnosis, cancer staging, tumor characterization, tissue oforigin, etc.), treatments and outcomes (such as therapy groups,medications, surgeries, radiotherapy, imaging, adverse effects,associated outcomes, and corresponding dates, etc.), and Genetic Testingand Labs (such as genetic testing, performance scores, lab tests,pathology results, prognostic indicators, and corresponding dates,etc.). Each of the fields (such as address, cancer staging, medications,genetic testing, etc.) may also have a plurality of subfields. Forexample, address may have subfields for type of use (such as personal,business), street, city, state, zip, country, and a start or end date(date that residency at the address begins or expires). Genetic testingmay have subfields for the date of genetic testing, testing providerused, test method (such as genetic sequencing method, gene panel), generesults (such as included genes, variants, expressions, etc.), tumormutational burden, and microsatellite instability. For medications,links as described above, including “has tradename” and “dosage of”relationships from any entity links may be traversed determine if thereis a relevant drug related to the candidate concept.

In another embodiment, a linked Entity may be received from the entitylinking stage of the intake pipeline. A query may be generated to searchover an ontological graph database having relationships includingmeta-synonymous links, synonymous relationships between links, and otherrelationships. For example, a linked entity may resolve to DuctalCarcinoma In Situ (DCIS) in the SnoMed dictionary. SnoMed may be thepreferred authority for cancers due to degree of comprehension anddetailed concepts included in the dictionary, expert opinion identifiesSnoMed as the best dictionary, or because SnoMed has the mostcomprehensive relationships between other dictionaries, is wellestablished, and meets requirements set forth by the institutionsmanaging the EMR/WEIR. A desired degree of specificity may haveselection criteria for normalized endpoints. For example, the selectioncriteria of a cancer type may include an Entity which identifies 1) thecancer site (where the cancer is located in the patient) and 2) thecancer type. An entity identifying DCIS may be limited to identifyingthe cancer type, but may not satisfy the cancer site selection criteriaand SnoMed may be searched to identify a normalized Entity whichsatisfies both criteria.

Normalizing DCIS may include navigating “is a” relationship links withinthe SnoMed database until an Entity is reached which identifies thecancer site as breast. For example, DCIS may be a tier three entitywhich “is a” specific type of cancer under “breast cancer.” Breastcancer may be a tier two entity which “is a” specific type of cancerunder the root “cancer.” Breast cancer may have a “has finding site”relationship to breast, which satisfies the selection criteria foridentifying the cancer site (breast) and the cancer type (breastcancer). However, to prevent loss of information, both the DCIS Entityand Breast Cancer Entity may be retained for the normalized Entity toaide in Entity Structuring described below. In SnoMed, relationshipsbetween cancers are structured such that there is a finite number ofjumps that “is a” links may traverse. Upon each traversal, an “is a”link may either result in a leaf node (traversed down), a terminal node(cancer with no further classification), or to the root (cancer).Traversal may stop at the first “is a” link which is encoded as aterminal node (such as based on the tier as described above, based off arelationship that exists in the node as described above, or that ispredetermined as a terminal node). Other relationships which mayidentify terminal nodes include, for example, in a medicine dictionary,Term Types “Ingredient” or “Preferred term” (such as TTY: GN for GenericDrug Name and TY:BD/BN/FBN for Branded Drug/Name or Foreign Brand Name,etc.), or the degree of specificity may be based off of relationships(such as “is a generic”, “is a brand name”).

Normalization queries are constructed to prevent out of bound searches,spurious results, and infinite searches. A representative normalizationquery of a medication may include:

MATCH p=(start:DICT {code:“DICT#AUI”}})−[:has_tradename|tradename_of*0 .. . 3]−(end:DICT)−[:has_umls_aui]→(aui2)←[:has_aui]−(descendant_cui)

RETURN DISTINCT descendant_cui.cui AS match_cui, length(p) ASgraph_distance

This query may return CUI's related to concepts which are linked toingredients identified in the medications terminal node list by up to 3trade names or generic names. In one aspect, a limit on the number oflinks which may be traversed and included in the query results may beincluded to reduce computational constraints (such as processor andmemory reservations). Queries may be optimized to provide both genericand trade name normalization endpoints, for example, by not specifyingor restricting the directionality of the [:has_tradename|tradename_of]portion of the query. Alternatively, queries may be directionallylimited to only traverse [:has_tradename|tradename_of] in a specifieddirection to limit the results which are generated as desired. Aterminal node entry for an ingredient to be encoded to in themedications valueset and may be encoded by including each respectivecode's dictionary (DICT above) and AUI into the query so that when a newentity is traversed, the AUI may be referenced with the list of terminalnodes.

A representative normalization query for a cancer type may include:

MATCHp=(cui:umls_cui)−[:has_aui]→(aui:umls_aui)←[:has_umls_aui]−(descendant:DICT)−[:isa*0. . . ]-<(:DICT {{code: “DICT#AUI”}})

RETURN DISTINCT cui.cui AS match_cui, length(p)−2 AS graph_distance

This query may return CUI's related to concepts which are lined as “isa” descendants of a given code (node). A terminal node entry for acancer type may be encoded in the cancer valueset and may be encoded asa primary diagnosis by including each representative code's dictionary(DICT above) and AUI into the query so that when a new entity istraversed, the AUI may be referenced with the list of terminal nodes.For cancer type queries, a return value may include the graph distanceof the path, which provides a qualifier for how many “is a” nodes are inthe path between the descendant and the queried code. After processingqueries for each node in the primary diagnosis valueset, there may existmany descendants that point to multiple parents. The resulting queryresponse of potential matches may be further curated according to thefollowing logic:

If a descendant D is generated by two ancestors A and B, but A and B arenot descendants of each other, then keep the mapping of D to both A andB; OR

If a descendant D is generated by two ancestors A and B, but A is also adescendant of B, then discard the mapping of D to B (because A is anearer ancestor).

In another embodiment, a concept candidate may be explored by more thanone query relating to the concept. For example, a concept candidate maybe explored/followed until a concept with a related structure (asdescribed in FIG. 6) is linked/normalized, then each of the associatedfields are queried in turn (Entity structuring is disclosed in moredetail, below).

An aspect of query generation may include tailoring queries to avoidspurious searches. For example, by recognizing directional relationshipswhich preserve the integrity of the source node, queries which preventerroneous destination nodes from being reached are preferred. Forexample, normalizing the Brand Name Entity for Tylenol may includetraversing the “ingredient of” relationship that Tylenol has. In onedirection, drugs for which Tylenol is considered an ingredient of may besafely explored. However, in the other direction, the ingredients ofTylenol may be explored. An ingredient which is shared between Tylenoland another drug may be linked by, for example, magnesium stearate whichis shared between Tylenol and Advil. A generic drug ibuprofen may thenresult from an unbounded query which does not restrict the traversal of“ingredient of” fields to prevent spurious drug hopping.

It may be advantageous to precalculate the results from frequent querysearches and cache the query results for speed. Caching precomputedqueries represent a tradeoff for the flexibility of results with thespeed at which they may be generated. Caches may include a node hopcount value that is used to resolve ties for least number of hops.Caching may be performed at the Entity Link stage and the EntityNormalization Stage. In a simplified representation, an Entity LinkingCache may include fields such as: Name of Concept Candidate, DictionaryCandidate Located In, and CUID. It may further be advantageous toidentify a structure category and corresponding fields based from theidentified CUID. Normalization may be directed to generate results whichrelate to the fields of the structure category identified. In anothersimplified representation, an Entity Normalization Cache may includefields such as: CUID, Medical Concept Structure, and normalized responsefor concept (Normalized CUID). Additional fields for either table mayinclude: graph distance (number of hops), preferred dictionary CUID,pre-defined entries (such as names, regions, categories), inferredstructure entries (such as diagnosis site, generic drug name), languageof text, match type (such as exact, exact but letter case mismatch,fuzzy matched, etc.), text type (TTY, described above), or other fields.

Normalized Entities may be further normalized to reduce known variancein results. For example, in a cancer type normalization, there may benumerous normalization endpoints which reference breast cancer in oneform or another that match the selection criteria of the normalizationalgorithm. A post-processing step to the normalization may be appliedwhich identifies, for example, when a cancer site is designated asbreast, and adjusts the final result such that all entries with a breastcancer site share the same cancer site code and same spelling “breast”.Other normalized results may include each main cancer site (brain, lung,liver, ovary, bone marrow, etc.), a predetermined catch-all for unknownsites, or known codes which are irrelevant to the normalization resultsand may be filtered.

Returning to FIG. 5, the Entity structuring pipeline 72 compiles each ofthe normalized concepts identified in the previous stage. However, giventhousands of pages of documentation within an EMR/EHR for a patient, thenumber of normalized entities that may be identified and resolved duringprocessing may number in the hundreds of thousands. The abstractionprocess as described above with reference to FIG. 5, may displayinformation about a normalized concept by providing various identifiedand populated fields. For example, with reference to the sentence “Thepatient was given Tylenol 50 mg at 10:35 am.,” the entity structuringpipeline 72 may encode the following fields:

Text: The entirety of the text (“The patient was given Tylenol 50 mg at10:35 am.”).

Medication: Identifying any medication mentioned in the text (Tylenol).Medications may be brand name or generic name. This field does notinclude information about the dosage or method of administration.

Active Ingredient: Identifying the active ingredients (acetaminophen) ofthe medication mentioned using a list such as a search table linkingdrug names to their active ingredients.

Dosage & Dosage Units: The dosage (50 mg) associated with the medicationmentioned. In the above example, identifying that the dosage as 50 mg isfairly straightforward by reading the sentence, but clinical data isoften printed in tables with a variety of structures that are not easyto infer. As such, normalizing the dosage and dosage units by separatingvalue 50 into the dosage field and string “mg” or by selecting a knownvalue entry for the milligram units within a list may be preferable.

Document & Page: The document and page where the text is found (ProgressNote 01_01_01.pdf and page 3).

UMLS_CUI: The CUI field (C0711228) of the UMLS entry corresponding tothe medication. The UMLS is a list of medical concepts and the UMLS_CUIrefers to the CUI field, which is UMLS' universal identifier. UMLS iscomprised of a number of independently maintained clinical dictionariesand ontologies (such as those for cancer diagnosis & treatment,dentistry, veterinarian medicine, etc.). That is, the CUIs are universalto UMLS, and there is only one CUI for Tylenol across all of itsconstituent dictionaries that enables UMLS to unite all of thesedisparate sources.

UMLS_AUI: The AUI field (RXNORM#4459) is the dictionary-specificidentifying code of the UMLS. Where the CUI is universal, and has thesame entry across all included sources, the AUI for Tylenol will havedifferent AUIs for each dictionary that it has an entry in.

Various fields, such as UMLS_CUI, UMLS_AUI, Medication, and ActiveIngredient may each be determined through the entity normalizationprocess by exploring the links to each of the Entities. The otherfields, such as dosage, dosage units, date/time administered, document,and page may not be determined through the normalization process.Instead, these other fields are provided to a Relational Extraction MLAfor extracting this information from the surrounding context or documentinformation (such as name, number of pages, etc.). For example, adocument named Progress Note 01_01_01 may be presumed to have a date ofJan. 1, 2001. Other concept candidates from the document may bereferenced to validate the date/time or select the date absent any othervalidating/corroborating information. For example, the time 11:35 am mayhave been provided as a concept candidate spatially near the “Tylenol 50mg” concept candidate. The Relational Extraction MLA may then identify11:35 am as the time the medication was administered based on theconcept candidate time being the next concept candidate in the list, aspatial proximity of the concept candidate, a new application of NLP tothe OCRed text string, or any combination thereof. Additionally, a pagenumber may be identified, for example, in a document that has 5 pages byreferencing the page number by performing an OCR of text at the bottomof the page or may be extrapolated by counting the number of pagesbefore the page the concept candidate was extracted from. Once eachfield of the medical data is identified through either the normalizationprocess or the structuring process and the relational extraction MLA,the patient/document may be ready to be classified according to eachnormalized and structured entity.

Returning to FIG. 5, the post-processing pipeline stage 74 may receive alisting of all the structured entities and generate a response/report.For example, a response may be a formatted into an output divided intoseveral sections, each section relating to, for example, the fields ofDiagnosis, Procedures, Radiology, etc., as discussed above. Under aDiagnosis header/identifier, structured entities relating to diagnosismay be summarized with the final normalized entity, information from theentity structuring, and any confidence values generated during theclassification and/or ranking/filtering. The response may include all ofthe sections with corresponding structured entities. The response may begenerated and output, such as as a word document, a spreadsheet, or aJavaScript Object Notation (JSON) file with each of the relevantsections and structured entities encoded therein.

The MLA and DLNN algorithms described herein may be implemented usingsupervised, unsupervised, and/or semi-supervised approaches.Patient/document classification based off of text classification is thegeneral task of processing text and identifying whether it belongs toone of many pre-defined groups (such as the above-referenced medicalfields). For example, supervised machine learning methods may be used toclassify patients as Male or Female, because many clinical documentsexist for patients whose genders are known. Exemplary non-machinelearning ways of determining a gender would be to apply a regularexpression for “Gender:” in text or “pt is a ## yo X”. It would be anexhausting endeavor to create a regular expression for every potentialcombination of words or characters that gender may be mentioned in textin order to be able to extract it using simple text matching. Instead, asimple heuristic component for classifying a gender may be to determinethe ratio of male vs female pronouns in text, under the assumption thatreferences in medical text are almost entirely describing the patient(as opposed to their family members or medical staff, who areoccasionally mentioned as well).

Similarly, a supervised machine learning method may require that thegender is known or provided for some batch of patients. The machinelearning method may then extract signals or features from the text thatare indicative of the gender. At that point, a Naive Bayes MLA may beutilized to, for example, identify the ratio of male vs female pronouns.The Naive Bayes MLA may determine the frequency of every word thatoccurs in any clinical document occurs in the male documents vs howoften the same words occur in the female documents in terms ofprobability (such as ‘he’ is 2% of words in male documents and 0.1% offemale documents). Once trained, for each new document to be classified,the Naive Bayes may use the generated probabilities/statistics todetermine the likelihood that a document falls within the malelinguistic probability distribution or the female distribution. Ageneral threshold value or comparison may be applied to determinewhichever probability is higher.

While supervised methods are useful when the training dataset has manyknown values or annotations, the nature of EMR/EHR documents is thatthere may not be many annotations provided. When exploring large amountsof unlabeled data, unsupervised methods are useful for binning/bucketinginstances in the data set. Returning to the example regarding gender, anunsupervised approach may attempt to identify a natural divide ofdocuments into two groups without explicitly taking gender into account.On the other hand, a drawback to a purely unsupervised approach is thatthere's no guarantee that the division identified is related to gender.For example, the division may be a between patients who went to HospitalSystem A and those who did not.

As a result, semi-supervised methods may be the most optimal approachwhenever there are a large number of unlabeled or unannotated documentsas well as labeled documents in the training set. EMRs/EHRs may beparticularly well-suited to this approach, because hospitals take careto note key health information for each patient. For example,considering a practical approach to applying a semi-supervised MLA,presume that an exemplary dataset generates a probability distributionsuch that “he” accounts for 2% of the words in male patients' documentsand 0.75% of female patients' documents. If these estimates were takenover a small number of patients (such as 100 pages of text total), but80 of these pages are from female patients, the probability distributionmay be quite susceptible to noise (erroneous weighing) and may generatewrong or undesirable results.

The unsupervised approach solves this by providing a number of documentsfrom patients whose genders unknown, effectively allowing the MLA tolearn something about language in general. Specifically, the MLAdetermines how frequent “he” may be presented in clinical text ingeneral. If the semi-supervised MLA identifies that “he” only occurs0.5% of the time, “he” may be occurring unusually frequently in thelabeled documents (such as at 2% and 0.75% probability distribution).For example, no ratio of male-to-female patients could balance out to0.5% given an initial probabilities of 0.75% and 2%. Instead, the MLAcorrects for the noise in the data set by applying the information thatthere were more female patients than male patients and accordinglyadjust the probabilities more strongly for the male probabilitydistributions than the female. A scaled probability distribution mayindicate that “he” occurs at 0.9% frequency in male patient files and0.1% in female patient files, so that the average distribution of “he”is 0.5%. The semi-supervised MLA may then accurately apply the heuristictechnique as a portion of the classification determination.

Machine learning algorithms and deep learning neural networks tend toprovide approximate solutions to any complex problem without a clear setof rules to constrain the problem through. MLA and DLNN are most usefulfor problems which are too difficult to constrain accurately to a fewsimple rules/constraints and excel at finding unique solutions to thesecomplex problems. These unique solutions may also include equally uniquebugs for edge cases of the unique solution, which may require finetuning to improve the performance of the MLA by adding better/moreaccurate/more representative training data, by tuning hyperparameters,or by improving or replacing the MLAs themselves.

In an exemplary model, as described below with reference to FIG. 11, atraining feedback loop 142 operates to improve the training data set byimproving the annotations of the edge cases and using the improvedtraining data to refine the MLA model itself. For example, an initialMLA trained on an initial data set may be only 75% accurate at its giventask. By directly utilizing the MLA in a platform where humans areentering data based on clinical documents for patients, edge cases(erroneous output) may be identified, the annotations surrounding thedocuments/patients of the edge case may be improved, and theimprovements submitted back into the MLA to further train the model toimprove accuracy. Regardless of whether the human agrees or disagreeswith the machine learning model's prediction/classification, the humantakes into account the prediction as well as other information in theclinical documents before making their final annotation. This finalannotation is utilized as the “gold standard” by which the MLA shouldoperate and can immediately add the labeled documents and thecorresponding annotation to the training data set to improve the resultswhen the MLA is trained in the future. Each edge case that is correctedby a human, even each additional question that a human answers above andbeyond the erroneous outputs may directly help the machine learningmodel answer the corresponding question correctly in the future.

The feedback process may be improved by adding the ability to collectdirect feedback from an annotator. For example, if the annotator agreeswith the machine learning model's prediction, then it may be presumedthat the prediction was correct. Conversely, if the annotator disagreeswith the prediction, it may not be clear why the MLA prediction waswrong. For example, the MLA may make an erroneous prediction if thedocuments were for the wrong person, if OCR errors exist whichconfounded the prediction, or if the model simply was not sufficientlytrained to make a correct prediction from the data in that instance.

Staying with FIG. 11, an exemplary system architecture is depicted. Inparticular, FIG. 11 depicts a scenario in which the system receivesdocuments, for example, from a clinical data vault 144, new documentsfrom an Attach system 146, or corrected documents via the Workbench 148(introduced below), uploads documents, and posts them to a Workflow 150.Workflow 150 may be a server that coordinates a number of tasks andmanages the intake of documents for the intake pipeline described inFIG. 5.

From there, the documents are posted to Attachments 146, for example,another server that stores sensitive files and authenticates all accessto those files. Concurrently, a copy of each of the documents is sent toa Converter 152, which patches each document with a viewable image, suchas a PDF, of the document. The system calls an OCR service 154, such asGoogle Cloud Vision or Tesseract, which runs optical characterrecognition on the documents. Alternatively, if the system determinesthat the document was already OCRed, a cached copy of the OCR documentis retrieved from a database (S3) 156. The viewable image file then istransmitted to the Attachments component 146, which links the originalfile with the image file. Similarly, a copy of a searchable text versionof the document is provided from the OCR service 154 to the Attachmentscomponent 146 to combine with the original document and the viewableimage from the Converter 152 and, if not previously OCRed, a second copyof the searchable text version is transmitted to the database 144 whereit is cached. The Abstraction Engine 158 and Abstraction Engine toolbox160 components utilize MLA and NLP to generate predictions.

Once the patient documents are processed in Workflow 150, Workbench 148,and then processed through OCR 154, raw OCR information may be pulledfrom the database. The processing intake pipeline stage forpre-processing and OCR occurs in these servers/processes. The systemalso may check the database to determine whether improved NLP modelshave been provided and retrieve any new or updated models. The systemthen applies the most current NLP algorithms and models to the raw OCRfiles. In this regard, patient data may be encoded differently dependingon the project for which it is being used, so the system may communicatewith a service (such as Valuesets 162 in FIG. 11) that includes one ormore templates to set forth how the OCR'd data should be abstracted andwhich values within that data are displayed for each field. Tabular andtemplate extraction may also be contained within the Valuesets database162.

The predictive data is then tailored for the given project from thetabular extraction applied, and those predictions then are posted to asecond database (such as the Abstraction Engine toolbox 164) for use byone or more additional applications. The Valuesets service 162 mayspecify a global encoding list for all of the concepts related to eachof the dictionaries/databases and the internal universal dictionary(such as medical concepts and fields described above). Using medicationsas an example, Valuesets 162 specifies all of the medication ingredientsthat may be beneficial for analysis.

By narrowing the search to a targeted list of concepts that areimportant to identify, overall processing speed of the architecture maybe improved. For example, UMLS metadata may be applied to determine that“Tylenol” is a brand name drug, “acetaminophen” is a generic ingredientas described above. When “Tylenol” is recognized as a medication,medication-specific queries may be processed to identify normalizationcandidates, for example, in the Abstraction Engine toolbox 160. If aquery returns that “acetaminophen” is in Valuesets 162 but “eucalyptusleaves” is not, any medication determined to be eucalyptus-based may beignored by the system.

Workbench 148 may represent a server for maintaining a user interface(UI) to implement a patient record analysis system responsible formanaging the flow of information between systems of the instantarchitecture and/or stage of the processing pipeline. An exemplaryhigh-level description of the UI may include three windows/panes, suchas a center pane that allows an abstractor to view patient documents forwhich the other two panes may display information relating to. A leftpane may be configured for entering the abstracted information,including fields (drop-down lists that are populated by Valuesets 162),dates can be entered and subjected to rules for validation (such as DOBmust be before date of death), singular fields (such as patient's genderor primary cancer diagnosis), repeatable fields (such as drugs thepatient took, surgeries, etc.), fields with sub-fields (such asmedication structured data, cancer diagnoses, etc. as disclosed abovewith reference to FIG. 6). A right pane may be configured for displayingAbstraction Engine 158 results. The way these are structured isdetermined by the Abstraction Engine 158 configuration. Category groupsfields at a high level and specifies, for example, four of themcurrently: Demographics, diagnosis, treatments, outcomes. Categorieshave many fields, which are what the abstractors are trying to entervalues for. These fields may also be expanded and collapsed. Whenexpanded, a list of values that the Abstraction Engine 158 predicted forthat field (and optionally, a confidence score specified for that value)may be shown. Fields can also have justifications tied to them, whichare text snippets that the Abstraction Engine 158 determines best showswhy the given value is correct for the given field. Given that many ofthe predictions are tied to the intake pipeline stages, the textsurrounding the identified concept candidate may be provided as thejustification.

Workbench 148, the patient record analysis system, may access and/orretrieve patient data from a patient record located in the Workflowscomponent 150, requested from the clinical data vault from the Workflowscomponent 150, or from the patient record including the documents thatwere stored in the Attachments storage 146. For each document, Workbench148 may also retrieve the corresponding NLP predictions from AbstractionEngine toolbox 160. Once abstracted, the final abstraction report anddata may be transmitted, via Workflows 150, to a clinical data vault.For example, the MLAs may have already providedclassifications/predictions for the patient that is being abstracted.The Abstraction Engine server 158 may have already processed all of thedocuments for the given patient, generated its predictions, and uploadedthem to Abstraction Engine Toolbox 160. The Workbench server 148 maythen retrieve the patient documents as well as Abstraction Engine 158predictions for each patient. An abstractor may use an interface ofWorkbench 148 for manual abstraction. The Abstraction Engine 158pipeline may be further optimized such that the Workbench interface 148also includes machine learning predictions for each template's fieldsand presents them to the abstractors (such as the fields of FIG. 6).Once identifications of relevant metadata for clinical concepts arefound in text, Abstraction Engine Toolbox 160 may generate predictions.Once entity normalization have been completed, a report may be generatedand provided to Workflows 150 for storing in the clinical data vault,for example, in a text file or a JSON format. This information may bepopulated for every medication that is identified in the patient'sclinical documents and may also be provided to the Abstraction EngineToolbox Service 160 for storing this information in a protecteddatabase. Other services can then query Abstraction Engine Toolbox 160by Patient or by Document and determine which clinical predictionsAbstraction Engine 158 has made. Abstraction Engine S3 156, AbstractionEngine 158, Abstraction Engine Toolbox 160, and Valuesets 162 togetherimplement the parser, entity linking, and entity normalization intakepipelines stages.

As mentioned above, the system periodically checks to make sure that theNLP/MLA models being used are most up-to-date (such as elements 76, 78,and 80 from FIG. 5). The system may include a Bootcamp subroutine 166for evaluating and updating the NLP and MLA models. In this subroutine166, the system retrieves clinical record documents from the clinicaldata vault 144, such as based on one or more unique user id's, onclinical features common to one or more patients, or any other criteria.The subroutine also may communicate with the Abstraction Engine S3database 156 to retrieve the raw OCR files corresponding to each ofthose documents, as well as the current NLP model. The system furthermay retrieve abstractor feedback (such as the feedback loop's erroneousresult corrections/annotations) from the toolbox 160. Each of theseinputs may be used to execute a training script to verify or update theNLP model. At that point, metadata relating to the updated model may becommunicated to the Abstraction Engine toolbox database 164 (such as forlater human inspection, model or data provenance, and/or long-termmetrics). Workbench 148 supports the ability for abstractors to tagAbstraction Engine's 158 incorrect predictions with a predetermined setof issues (such as documents are from wrong patient, OCR errors, wrongentity linked, correct concept candidate, wrong entity linked, correctconcept candidate but hypothetical reference in document cannot beconstrued as haven taken place, etc.). For example, in the case ofpatients whose predictions are incorrect because ‘Documents are forwrong patient’, the Abstraction Engine Bootcamp 166 may ignore thesepatients when training future MLAs to understand gender or mayinstantiate a specific training phase to train the current MLAs topredict which patients have documents from multiple patients and excludefrom training and/or flag all patients which have documents from wrongpatient for independent abstraction.

Similarly, other tags such as ‘Bad prediction due to OCR error’ may beapplied as feedback on a given OCR software/service, which means thesystem can implement various OCR services and use abstractor feedback todetermine the highest quality OCR service 154 from various competitors.Abstraction Engine toolbox 160, Workbench 148, and Workflows 150together implement the Entity structuring and post processing intakepipeline stages.

Workbench 148 facilitates and incorporates human abstraction byproviding prediction justifications and confidence metrics alongside thepredictions. A number of issues arise when providing an abstractor withonly a single list of possible answers and corresponding confidencevalues. For example, an abstractor may not be provided with anyreasoning about how the predictions or confidence values are calculated,or it may not be clear when an abstractor should trust the NLP modelsand when they should take a deeper look into the patient record becauseit is difficult to know what confidence level is needed before an outputneeds to be verified for accuracy. Instead of making this decision thesole responsibility of the abstractor, Abstraction Engine 158 isdesigned to provide justifications for its predictions in the form oftextual contexts that are determined to indicate that a prediction iscorrect.

Following the example of structuring a full medication entry thatincluded a Text Context field (FIG. 6), additional processing maydetermine whether the fully structured concept is a positive mention(such as it is not related to a family member's previous illness ortreatments, it is not a hypothetical treatment proposed by a doctor, itis not a diagnosis unrelated to the patient that happens to be mentionedin supplemental literature, etc.) and maintaining links to text contextmay be a useful justification to the positive mention. Thisdetermination may be processed through other text classificationalgorithms that use the contextual information to identify whether theconcept mention is positive or negative. For example, the simplestimplementation may include a pattern-based system configured to ignorediagnoses in contexts such as “{mother/father/sister/etc.} has a historyof {disease}.” While these phrases may be considered in the NLPalgorithm itself, error checking may involve repeating the process inlow confidence predictions, or providing additional algorithms with textclassifiers that utilize the additional textual context. Anotherembodiment may involve aggregating all of the mentions of a primarycancer site which may also include all or some of the textual contextsfor those mentions, which can provide the abstractor with confidencethat the prediction was correct without manual intervention.

Turning now to FIG. 12, a patient upload process of the instantarchitecture is disclosed. In particular, this figure illustrates aprocess in which Patient documents may be uploaded by Extract,Transform, Load (ETL) Tool or a Q-Manager. Q-Workflows 150 may post thedocuments to Attachments 146. A Converter 152 may patch the documentswith viewable PDFs. OCR 154 may run either an OCR service such as GoogleCloud Vision or Tesseract to OCR documents or, if the document waspreviously OCRed, it may retrieve a cached copy of the OCR. The systemthen may receive a response from S3 156 instead of OCRing it again. OCR154 may patch the documents with a searchable text version of the PDFs,and OCR 154 may cache the raw OCR files to the Abstraction Engine S3bucket 156.

Turning now to FIG. 13, a prediction generation process of the instantarchitecture is disclosed. In this aspect, once the patient documentsare processed, the Abstraction Engine 158 may pull raw OCR files fromits S3 bucket 156, check S3 156 for improved NLP models and pulls themif necessary, run the documents through its current NLP pipeline andmodels, pull project-specific templates from Valuesets 162, tailor itsfinal predictions for the given project, and post those predictions andrelated metadata to the Abstraction Engine Toolbox 160. In this regard,patients may be encoded differently in each project, so Valuesets 162may be a service that coordinates project encodings (such as whichfields are abstracted, which values are displayed for each field).

Turning now to FIG. 14, an abstraction process of the instantarchitecture is disclosed. In this aspect, when a Q-Workbench user loadsa patient, Q-Workbench 148 may pull the patient record from Q-Workflows150 (Q-WF), including patient documents which are passed fromAttachments 146 through Q-WF 150. Q-Workbench 148 also may pull thecorresponding Abstraction Engine predictions from Abstraction EngineToolbox 160 (if the predictions are available). The abstractor mayabstract data field by field and pass patient data to Q-WF 150. Patientsmay provide direct feedback about specific NLP predictions, which willbe passed directly to Abstraction Engine Toolbox 160. And the abstractormay submit the final abstraction report and data makes its way throughQ-WF 150 to the Clinical Data Vault 144.

Turning then to FIG. 15, a feedback loop and training process of theinstant architecture is disclosed. In this aspect, the AbstractionEngine Bootcamp 166 may periodically update Abstraction Engine NLPmodels. Specifically, the Abstraction Engine Bootcamp 166 may beinitialized by a script or a periodic update protocol. The AbstractionEngine Bootcamp 166 also may pull: clinical records from the ClinicalData Vault 144 for a list of patient UUIDs specified by script/protocol,the raw OCR files that correspond to each of these patients' documentsfrom the Abstraction Engine S3 bucket 156, and existing NLP models fromS3 156 (some models can be trained multiple times and improve over manyiterations of new data). Abstractor feedback may be pulled fromAbstraction Engine Toolbox 160 into Abstraction Engine Bootcamp 166 foradditional training info. The Abstraction Engine Bootcamp 166 mayexecute its training script and post NLP models to S3 and also postmodel metadata to Abstraction Engine Toolbox 160 for human inspection,model/data provenance, and long-term metrics.

The systems described above may have multiple uses that are beneficialto clinicians and researchers involved in the treatment of diseases,research into diseases, and data analysis involving disease. One exampleis in the field of clinical trials. A clinical trial is a research studyto determine the safety and efficacy of a drug, device, biologic, orother potential treatment. Clinical trials often have inclusion andexclusion criteria, whereby a patient must meet all of the inclusioncriteria and not have any of the exclusion criteria in order to enrollin the study. Many clinical trials have specific criteria that can bedetermined only after close examination of the medical record. Forinstance, an example of inclusion criteria for a study of chemotherapyof breast cancer subjects might be postmenopausal women between the agesof 45 and 75 who have been diagnosed with Stage II breast cancer. Anexclusion criterion for this study may include a positive identificationfor abnormal renal function, if, for example, one or more of the drugsused as treatment in the study are nephrotoxic. A medical institution,such as a hospital, may have many patients who are eligible for thestudy, but require the system described above in order to parse theirEHR in order to prepare a list of patients who are eligible toparticipate in the study.

Another example relates to the development of synthetic control arms forclinical trials. In a clinical trial, a group of patients (called the“control group”) receives standard of care treatment while a secondgroup (the “experimental group”) receives an experimental treatment(such as a study drug). Often, a study is “blinded” meaning the patientswho enroll in the study do not know if they are part of the controlgroup or the experimental group. It can be difficult to recruit patientsto clinical trials because many patients wish to ensure they are part ofthe experimental group. An institution may utilize the systems andmethods described herein in order to create a list of structured datafrom each patient in the EHR who meets the inclusion/exclusion criteria.By leveraging the existing data of patients who do not qualify for theclinical trials, a propensity based model may supplement the clinicaltrial data as the control arm of the study. These patients may beconsidered the control group, and their health data as captured instructured format may be utilized as the control arm of the study. Inthis way, a separate enrolled control group is not needed for the study,and the patients who enroll may all be made part of the experimentalgroup.

Another example relates to data analysis of an institution's EHR. Manyinstitutions, such as hospitals, retain patient health information infree text that is not easily searchable for patterns in treatment oroutcomes. Using the systems above, institutions may be able to createstructured data sets with data elements that permit the institution toconduct sophisticated data analysis to look for data trends. Such trendsmay indicate best practices in particular departments, or may indicateareas of concern that require the institution to conduct furtherinvestigation. For example, the institution may utilize the systems andmethods described above in order to determine which patients are beingprescribed which medications at which dosages. The systems and methodsmay be used periodically (for instance, on a quarterly basis), toanalyze utilization rates. As another example, the institution mayutilize the systems and methods described above in order to characterizethe outcomes of patients with respect to treatments which they have beenprescribed and undertook while under the care of the institution. Theanalysis may be conducted in a way that the structured data generated bythe systems and methods described above omits certain data elements inorder to ensure that the structured data is de-identified or thatprotected health information is securely maintained, encoded, orremoved. For instance, name, address (all geographic subdivisionssmaller than state, including street address, city county, and zipcode), elements (except years) of dates related to an individual(including birthdate, admission date, discharge date, date of death, andexact age if over 89), telephone numbers, fax number, email address,Social Security Number, medical record number, health plan beneficiarynumber, account number, certificate or license number, any vehicle orother device serial number, web URL, Internet Protocol (IP) address,finger or voice print, or photographic image of the patient, may all beomitted from structured data fields. Alternatively, or in addition, theresulting data may be run through a statistical system to ensure thereis a very low chance it contains identifiable health information.

In another example, an institution may utilize the systems and methodsdescribed above to conduct automatic quality checks on the informationcontained in its medical record. For instance, the institution may usethe systems and methods to compare information in one section of themedical record with information in another section of the medical recordto ensure consistency between the records in each section. As anexample, imaging reports on cancer tumors can contain radiologyinformation about the tumor (such as its size), while a radiology reportprepared by a physician may also contain similar information. Thesystems and methods described herein may be used to ensure that theimaging report (for instance, the tumor diameter is 2 cm) is consistentwith the information as the radiology report (for instance, the tumordiameter is 2 cm). If the information is different, an alert may betriggered to have a clinician review the record further.

In another example, other types of records could be used instead ofpatient records to create a structured set of data from unstructuredinformation. One type of record that could be analyzed using the systemsand methods described above is a scientific journal publication. Manypublications disclose information about new and potentially promisingtreatments in cancer and other diseases. Other publications discloseinformation about existing treatments that may be useful for newlyindicated diseases. The systems and methods described herein may be usedto automatically generate a list of structured data from a scientificpublication (for instance, it may generate a list of structured dataindicating that a certain drug is effective at a certain dosage for acertain class of patients). The list of structured data may be combinedin a knowledge database comprising other similar lists of data.

In another example, the systems and methods described herein may producestructured data that can be aggregated, and the results of theaggregation may be analyzed for comparative purposes. One exemplary useis for population health purposes. For instance, the systems and methodsdescribed herein may be used to compare aggregated structured data fromone institution with aggregated structured data from another institutionor another group of institutions. Such comparison may be useful whendetermining medication utilization rates; duration of inpatient stays;rates of readmission; types and frequencies of diseases, such ascancers; or other indicators. As another example, the systems andmethods described herein may be used to compare aggregated structureddata from one geographic area with aggregated structured data fromanother geographic area. Structured data from an institution or ageographic area may be aggregated using methods known in the art.

In exemplary embodiments, processing of the electronic document capturemay be performed on the mobile device 10 or may be sent to a cloudserver to reduce the demand on the mobile device's battery andprocessing resources. For example, the mobile device may obtain anelectronic data capture and provide an image of the capture to the cloudserver for processing according to the steps disclosed herein.Alternatively, the mobile device may obtain an electronic data capture,perform region capture, and perform OCR on the capture to extract textfrom the captured region. The mobile application may then provide onlythe extracted text as well as text identifiers to the cloud server forprocessing. Exemplary text identifiers may include the Form identifieror document identifiers discussed above as well as a region identifierwhich identifies which region the extracted text corresponds to. In eachof the above embodiments, the cloud server may return the extractedpatient information, such as patient name, diagnosis, treatment, orsequencing information, to the mobile application for display andverification by the user.

In one embodiment, the application may include error detection of theelectronic document capture. For example, the application may detectthat an electronic data capture is of poor quality, and request that theuser rescan the page. Such quality detection may be performed byevaluating character quality, for example, comparing density of thesolid lines or the fuzziness of lines, checking the whitespace aroundperceived collection of words for artifact detection. In anotherembodiment, the application may detect that a page of the document isincorrectly scanned (such as the user either scanned the wrong page ofthe correct document or a page from a different document). Exemplarydetection may be performed by comparing the expected layout of the page(arrangement of document features in the predefined model) with theelectronic document capture. For example, if a table is present in thefeature list of the identified document, but is not located in theelectronic document capture at the expected page, a general error may beflagged to indicate to the user that the expected page was not captured.Furthermore, features which are tagged as optional may be ignored duringform verification if they are not present.

Certain error detection may not be easily performed. For example, geneshave a plurality of possible variants and each variant further haspossible representations. As discussed above, redundant informationstored in multiple features of a report, or even report appendices, maybe referenced to provide a more robust error detection. However, it maynot be possible to automatically detect when a genetic variant is anerror from OCR or not.

This problem may be resolved by cultivating a growing set of knowledgeand insights around genetic variants and their related attributes. Forinstance, the application may be able to programmatically differentiatevalid vs. invalid variants (correct: EGFR, incorrect: HFGR) by queryinga genetic variant database for observed and classified variants for eachgene. A database may store knowledge and insights around geneticvariants and their related mutation effects currently consists of bothinternally managed and externally sources, for example, COSMIC (theCatalogue of Somatic Mutations in Cancer), NCI's Clinvar, or gnomAD (theGenome Aggregation Database). This reference data may be used toclassify a genetic variant according to data elements such as over orunder expression or other deviation in gene expression counts, singlenucleotide variants, copy number variants, or coding mutations andfusions. Additionally, various other classifying attributes may be foundin the set of knowledge and insights, for example, the chromosome onwhich the variant was detected, whether a variant is therapeuticallyactionable, or if it is germline. By using a combination of theredundant features in the electronic document capture and reference datasets, a variant identified in source documents by the application can beevaluated for validity.

In one aspect, the application or a cloud server in communication withthe application may query the database via its API to validate whether arecognized gene and variant combination is valid/known or if it isactually an unrecognized variant, an OCR introduced error, or if theunknown combination originated from the clinical documentation and/ortext. Known genes and variants have matches, unrecognized variants maynot have matches or one that has not been identified, sufficientlyclassified, or expertly-curated by the scientific community. An OCRerror, however, results from imperfect technology for identifying andextracting text from images and/or documents.

Turning to FIG. 16, the user may validate the information captured froma document (such as the document of FIGS. 4A-B) by confirming thepatient details are correctly populated in the fields and initiating aquery of the patient cohort. For example, the application may include areview interface 170, through which the physician may confirm that thename populated in text field or drop down 172 is the patient's and isspelled correctly, the diagnosis in text field or drop down 174 is thepatient's and is spelled correctly, the collection date of the report indate field, text field, or drop down 176 is the report's, and each ofthe gene identifiers and corresponding variants in fields 178A-C areconsistent with the report data. In the event that the capturedinformation is inconsistent with the document from which it wascaptured, the application may permit manual editing of that information.For example, if the patient name was captured as “Jane A. Dot,” tappingor pressing and holding the patient name field may open an editorpermitting the user to make the necessary changes. Similarly, selectinga gene identifier icon, such as the oval in any of fields 178A-C maypermit the user to modify the mutated gene identified by the MLA in theevent it does not match the captured document. Selecting that icon mayopen a search dialog box and a keyboard on the mobile device in order toreceive user input of the specific mutation. If the correct gene wasidentified as mutated, but the specific variant within the gene does notmatch that listed on the document, the user may tap or press and holdthe portion of field 178A-C outside the oval. Doing so may open asimilar keyboard as for the gene identifier. Alternatively, theapplication may open a list of possible variants for the identifiedgene, the list being scrollable in the event that its full contents donot fit on the screen all at once. It should be understood thatsuggested field types above, including text, drop down, or date aremerely representative of the types of fields that may be implemented andshould not be construed as limiting each respective field to those typesas disclosed above.

A button or gesture may be used to add a field to the data which mayhave been omitted by the extraction process above. For example, the usermay press and hold on the blank space below the last entry to cause anew field to appear, or the user may place a finger on two consecutivefields and spread them apart to cause a new field to appear betweenthem. The newly added field may appear at the bottom of the list and theuser may drag and drop the field into the appropriate place on theapplication interface 10. The user may confirm the information iscorrect by selecting button 180 or by initiating a corresponding gesture(such as using three fingers to swipe interface 170 to transition to thenext window of the app). Upon validation of the information, theapplication may also store a copy of the data (after deidentificationand/or removal of protected health information) to include in futurereports. New fields and updated fields may be processed again for entitylinking and normalization to ensure that each field is accuratelycurated for generating the query and storage.

The initiated query may be generated by extracting the data from eachfield of the application and generating a query with the extracted data.For example, each field may include both the text that has beenconfirmed by the physician and the entity linking data identifying thematch to a concept in the medical dictionary as described above. Thefields may be added to a container, object model used by the underlyingdatabases, a nested database/dictionary, or other format before encodingand transmission. Transmission may be received and processed at anendpoint of a cohort repository and engine for processing patients andgenerating the cohort report.

In another embodiment, the initiated query may be received at a databasestoring aggregate information from patients of one or more physicians.Fields of the query may be extracted and processed by the database toidentify a group, or “cohort”, of patients in the database who aresimilar to the physician's patient. Both the text and the linked entitymay be stored to ensure the medical concept/relevance of each entry isaccurately recorded. Similar patients having features matching one ormore of the features included in the query may be identified and addedinto a cohort of similar patients. For instance, the initiated query mayinclude a gene identifier that reflects a genomic mutation present onthe patient's NGS sequencing report or other document which wasinitially image captured. A gene identifier may be a gene name,abbreviated gene name, or another label that indicates a specific gene.The cohort of similar patients may be then selected, at least in part,by identifying those patients in the database of aggregate patientinformation with the same genomic mutation. For example, if a patient'snext-generation sequencing report indicates that the patient has a BRAFmutation, the database of aggregate patient information may be queriedto identify all patients in the database whose records indicate theyalso have a BRAF mutation.

The medical information of the cohort of similar patients, or summaryanalysis thereof, may then be provided to a report generator forprocessing to identify trends of the patients' case histories duringdiagnosis and treatment and generate a cohort report. The cohort reportmay be displayed to the physician, for instance on a screen of themobile device 10.

As seen in FIGS. 17-19, the application may display the cohort report ofsummarized medical information, which that may help the physician make atreatment recommendation to the patient. When the summarized medicalinformation supplements the information on the initial report, itprovides new information to the physician, not present in the initialreport, which can help the physician make a more informed treatmentdecision that may result in improvements to the patient's care, such asimproved patient outcomes and greater value of care. FIG. 17 depicts afirst cohort report 182 including summarized medical information aboutthe cohort. The summarized medical information includes one or moretreatment regimens 184 administered to patients in the cohort, alongwith relevant response data 186 for each regimen. FIG. 18 depicts asecond cohort report 192 including the same treatment regimens 184 as inthe first cohort report 182, this time with summarized medicalinformation including relevant adverse event data 194 for each regimen.FIG. 19 depicts a third cohort report 196 depicting summarized medicalinformation in the form of potential clinical trial matches 198 for thepatient. Each of these cohort reports are discussed in greater detailbelow. It should be understood that the types of summarized medicalinformation detailed in FIGS. 17-19 are exemplary, and other types ofsummarized medical information of the cohort may be presented to theclinician, such as immunotherapy results, radiology imaging results (forinstance, the average progression of tumor size in patients in thecohort), pathology imaging results, other imaging results, outcomesinformation (such as survival information), medical billing information(for instance, the cost of care for patients in the cohort), etc.

After data has been validated by a user (a clinical data abstractor,nurse, physician, etc., that has ensured that a patient's informationhas been accurately extracted from the electronic document capture ofone or more patient reports), the extracted patient information may bestored in a common and structured data format either on a mobile deviceor in the cloud. An example of a structured data format includes FHIR,OMOP and/or other priority data models that support the representationof numerous attributes (such as demographics, diagnosis, treatments andoutcomes, genetic testing, assessments and labs, etc.). This structureddata may then be shared back with a health system's EMR or EHR as partof a patient's record or with certain third party applications thatsupport the ingestion of this type of data (such as Apple's HealthKit,ResearchKit, CareKit, or internal proprietary format for each database,etc.). More than one database may receive the structured data or arelevant portion thereof. For example, a patient cohort database mayreceive all of the patient information while a genetic database may onlyreceive the genes expressed by the patient, the diagnosis of thepatient, and/or other patient information also included in the geneticdatabase. The structured data may also be provided to a master patientindex which may identify if the patient already has entries from priorinteraction with the database through either the application or anotherpartnered institution. The new information may be associated with thealready existing patient data or if no matching patient is found a newpatient may be added. Other exemplary databases include variantdatabases to store genetic variants, or clinical trial managementsystems and databases which track patients who are undergoing treatmentas part of a given clinical trial. A notification may be provided to theuser spanning multiple different delivery mechanisms including a directpush notification to their mobile device, an SMS or text message sent totheir mobile device, an in-application notification as part of theapplication user interface and/or via an accompanying email that may besent to any associated email address corresponding to their valid userprofile. An analytics module may be present and connected to any of theabove databases. The analytic module may be the same as described inU.S. Provisional Application No. 62/746,997, incorporated by referencein its entirety, including the analytical tool that enables theoncologist to explore prior treatment responses of patients that havethe same type of cancer as the patient that the oncologist is planningtreatment for in light of similarities in molecular data between thepatients. Furthermore, the cohort analytics identifies different cancerstate filters to be applied to the system database thereby changing theset of patients for which the system presents treatment efficacy data toexplore effects of different factors on efficacy to lead to newtreatment insights like factor-treatment-efficacy relationships. Tofurther the pursuit of new cancer state-treatment-efficacy explorationand research, in at least some embodiments it is contemplated thatsystem processors may be programmed to continually and automaticallyperform efficacy studies on data sets in an attempt to identifystatistically meaningful state factor-treatment-efficacy insights. Theseinsights can be confirmed by researchers or oncologists and usedthereafter to suggest treatments to oncologists for specific cancerstates. Trends, outliers, insights, and other metrics may be analyzedand stored for later use. Additionally, metrics may includepathogenicity of variants, genomic phenotypes, organoid response totreatment in a laboratory for efficacy calculations, radiomic andpathomic features from an imaging lab, tumor mutation burden,microsatellite instability status, immunological target expression,resistance risks, immune system infiltration, PD-LI expressions, as wellas any trends, outcomes, and insights that may be made between them.These metrics, and more, may be provided to the cohort report below forinclusion as additional data. Additional data may be include general NGSmedical information or field specific NGS medical information such asoncological NGS medical information for cancer patients. Oncological NGSmedical information may include a diagnosis of cancer, metastasis, orother diagnosis, types of treatments including medications andtherapies, duration and dosing of treatments, and for tumors, the tumorand/or patients non-tumor molecular structure, genes, variants, fusions,copy number counts. General NGS medical information may include the“normal” genome of a patient molecular structure, genes, variants,fusions, or copy number counts. General NGS medical information mayinclude any details which may be shared between NGS reports fordiffering illness, disease, and cancers.

FIGS. 17-19 detail different embodiments of the cohort report. FIG. 17is one aspect of the cohort report and may feature particular treatmentregimens 182 which have been prescribed to similar patients, howfrequently the treatment occurs in the subset of similar patients (the“incidence”), and a visual or numerical representation of the patientresponses to the treatment 186. Treatments may include singular drugs,therapies, or combinations of drugs and/or therapies. For example, whileFIG. 17 displays five separate regimens comprising singular drugs(vemurafenib, perifosine, miltefosine, erlotinib, and rapamycin), inanother instance, a regimen may comprise a combination of two or more ofthose drugs, or one of those drugs plus radiation or another therapy. Incertain embodiments, combinations of drugs and/or therapies may bedifficult to display in one line. In such cases, the combination may beterminated early with an ellipsis and the user may expand thecombination by selecting it in the application. Upon selection, thecorresponding entry may resize to display the full combination. Thedisplay of one or more of FIGS. 17-19 may include an information icon188 next to one or more of the treatment regimens, the selection ofwhich may launch a web browser on the mobile device 12 or another screenin the application 10 to provide more information about the selectedregimen. Alternatively, the text of each regimen or the field or row inwhich the regimen is shown may include an embedded hyperlink,accessible, such as by pressing and holding on the text of the regimen,hovering over the regimen using the cursor discussed above, etc. Ineither case, selection of the information icon or selecting the fieldmay launch a drop down, a hover menu, a web browser or another screen inthe application to provide further information about the selectedregimen. For example, FIG. 17 includes a drop down 190 providing theuser with various options related to a selected regimen (“Rapamycin”),including the ability to access select reference materials, to searchone or more databases of information (such as PubMed), and/or to editone or more fields of the captured document (for example, to correct anerror if the physician notices during reading the report that treatmentsshown correspond to the wrong patient information).

The cohort report may contain all resulting treatment regimens from thesubset of similar patients, the treatments that have a statisticallysignificant incidence, or all treatments which meet at least a minimumthreshold of patients. Such threshold may be based off a predeterminednumber of patients, or may be based upon the number of patients in eachof a plurality of treatment regimens, such that only regimens which havea certain percentage of the patients of the whole cohort are included,for example, by summing the number of patients in the treatment regimensand only displaying treatments with at least 5% or higher of the totalpatients. The lower (5%) and upper bounds of this threshold may bedetermined based off of the number of regimens included in the reportand their incidence rate as well. In another example, if severalregimens have patients by the tens or hundreds, a regimen with only fivepatients may be excluded from display. The values may use the average,the mean, the average of the mean, or other calculations to identifywhere the lower and upper threshold cutoffs should be placed. Anexemplary numerical description may quantify the number of patients whoreceived the treatment, the number of patients who responded favorablyto the treatment, the number of patients who had no change from thetreatment, and/or the number of patients who responded unfavorably tothe treatment, identified as “Complete Response (CD), Partial Response(PR), Stable Disease (SD), Progressive Disease (PD)”, respectively. Inan exemplary visual representation, a color coded graph 186 may beprovided to the user to visually represent the same features as thenumerical description outlined above. For example, patients whoresponded favorably may be color coded green and given a distribution ofthe graphical representation directly proportional to the percentage andpatients who responded unfavorably may be color coded red and given adistribution of the graphical representation directly proportional tothe percentage.

FIG. 18 is another aspect of the cohort report, with similar layout andinformation provided as FIG. 17. In FIG. 18, however, the applicationmay provide a therapy response summary conveying adverse eventinformation 194 for each of the regimens 184 identified in FIG. 17. Inaddition to displaying similar patients' responses to treatment regimensthe system may return the incidence of adverse events incurred bysimilar patients respective to those treatments. These adverse eventsmay be categorized by the type of event (such as neutropenia, nausea,headache, hallucinations, fever, fatigue, depression, cardiac disorders,etc.) and/or by the grade of its severity. (Mild, Moderate, Severe,Life-Threatening, Death). There are thousands of classified adverseevents, and the application may be configured to display events based ontheir respective grade of severity, rather than a name-by-name basis. Inanother embodiment, the user may select the field of the medication tosee the adverse events that contributed to the grade of severitydisplayed alongside the medication along with the number of incidencesand the grade of severity associated with the adverse event.

FIG. 19 is still another aspect of the cohort report which mayspecialize on clinical trials. Based upon the key health informationextracted from the electronic document capture, clinical trials that areavailable to the patient may be identified and displayed. For eachclinical trial, details 198 associated with the name of the clinicaltrial, geographic location of the facilities administering the trial,treatments associated with the trial, inclusion/exclusion criteria forpatients who may participate in the trial, and other relevantinformation may be included in the report. Additional information may beextracted from the electronic health or medical records associated withthe patient when the query is processed that further allow the inclusionand exclusion criteria of a clinical trial to be evaluated. For example,the electronic document capture may be missing key health informationpertaining to the patient's medical history, such as medical historyrelating to whether the patient has taken a drug as part of treatment orhas undergone chemotherapy, and the patient's medical history may bereferenced to determine eligibility for clinical trial inclusion andexclusion criteria.

Swiping between each report may be performed by pressing the tabassociated with the report from the user interface or through gesturecontrols. For example, a user may swipe the current page to the left orright to swap between respective reports.

The application as described above may be useful in multiple aspects ofmedical care. For example, the following use cases may be representativeof the various ways in which the application may be employed, althoughit will be understood that the application should not be limited solelyto the following use cases.

1: Report Supplementing

Turning to FIG. 20, one method 200 for implementing the present systemis depicted. At step 202, the mobile device may be used to capture adocument such as a NGS report, the document including medicalinformation such as sequencing information about a patient. At step 204,an entity linking engine may be used to extract at least some of thatinformation, such as using the techniques described above. At step 206,that information then may be provided to one or more data repositories,such as in a structured format.

Information from the electronic document capture may be supplemented inthe cohort report with additional supplemented structured data. Forexample, a genetic sequencing report such as the report of FIG. 4 mayidentify a genetic mutation that is present in the patient's DNA and mayfurther list treatments available for the genetic mutation. A newtreatment may become available after the report is generated but beforethe physician meets with the patient to discuss the report results.Notification of that treatment may be received, as at step 208. At step210, the above-described mobile application may supplement the reportinformation and alert the physician to the new treatment for theidentified genetic mutation that may have been otherwise overlooked.Additionally, the report may be supplemented by providing access, viahyperlinks or otherwise, to recent articles, publications, or otherrelevant information that may aid the physician by providing context,background information, or access to recent publications that addressdetails of the report, the other articles, publications, or otherrelevant information being structured using similar techniques forconvenient retrieval. Other medical topics of interest may also bereferenced, such as new cell-based therapies (such as immuno, viral, orvector delivery methods) available or new therapies available (such ascheckpoint blockades for accelerating immune response, cancer vaccines,etc.). Furthermore, a physician may make treatment decisions and treatthe patient according to treatments identified as having a likelihood ofsuccess across other patients having similar molecular and clinicalfeatures to the patient. Additionally, a physician may identify that atherapy has not had success for the patient and may desire to replacethe unsuccessful therapy with one of the report supplemented therapieswhich is expected to have a likelihood of success. In order to receivepreauthorization from or to validate a claim with the patient'sinsurance (e.g., by indicating the medical necessity of the treatment),the physician may reference the supplementary information, such as theprogression free survival rate of similar patients or a publicationrecently linked on PubMed in their requests to the insurance company.After receiving such pre-authorization or medical necessity indication,the physician then may administer the therapy or other treatment.

2: Training Set Inclusion

The mobile application described above may also be useful when pairedwith the existing clinical abstraction training sets for machinelearning algorithms driving the abstraction process. Thus, turning toFIG. 21, another method 300 for implementing the present system isdepicted. At step 302, the mobile device may be used to capture adocument such as a NGS report, the document including medicalinformation such as sequencing information about a patient. At step 304,an entity linking engine may be used to extract at least some of thatinformation, such as using the techniques described above. At step 306,that information then may be provided to one or more data repositories,such as in a structured format. At step 308, an active learning elementof the machine learning engine may identify a section of the electronicdocument capture for which the algorithm did not have a high confidenceof the predicted output. The electronic document capture may then belabeled as a training input and added to a respective training data set,as at step 310. The improved training set may then be used to train amachine learning algorithm to generate improved results. Many documenttypes (such as genetic sequencing reports) include relevant attributessuch as genes, variants, etc., that would normally be abstractedphysically by hand may then be automatically extracted according tothese characteristics and paired with additional clinical and phenotypiccharacteristics (such as demographics, diagnosis, assessments, labs,etc.).

3: Database Comprehension Validation

Turning to FIG. 22, another method 400 for implementing the presentsystem is depicted. At step 402, the mobile device may be used tocapture a document such as a NGS report, the document including medicalinformation such as sequencing information about a patient. At step 404,an entity linking engine may be used to extract at least some of thatinformation, such as using the techniques described above. At step 406,that information then may be provided to one or more data repositories,such as in a structured format. Further, the disclosure may also aid inthe ability to fully assess the quality of a given structured clinicalrecord by comparing extracted information against other structured data,as at step 408. For instance, the mobile application may indicate thepresence (or absence) of various molecular biomarkers (such as TP53)that indicate whether other various and/or observed clinical attributesare appropriate. For example, molecular biomarkers like KRAS may bepresent in only a certain subset of cancer types (such as pancreaticcancer). This capability can improve data integrity by identifyingunusual and/or incorrect structured clinical data that may have beenabstracted and/or ingested directly from third parties via variousintegration mechanisms, as at step 410, and by identifying andhighlighting discrepancies between the extracted data and other relevantdata in the system separate from that extracted data, as at step 412

4: Radiology Report Supplementing

Turning to FIG. 23, still another method 500 for implementing thepresent system is depicted. At step 502, the mobile device may be usedto capture a document such as a NGS report, the document includingmedical information such as sequencing information about a patient. Atstep 504, an entity linking engine may be used to extract at least someof that information, such as using the techniques described above. Atstep 506, that information then may be provided to one or more datarepositories, such as in a structured format. The extracted data thenmay also be useful when attempting to determine and/or unite clinicaland/or phenotypic attributes with observations from pathological and/orradiological imagery, such that the system may link the extracted data,via its structuring, with structured clinical patient data received frompathology reports, imaging features, and/or other imaging sources, as atstep 508. Often, the ability to obtain more context about a givenpatient and/or diagnosis is crucial in determining whether imaging is ofa sufficient quality for computing radiomic attributes (such as surfacearea, volume, etc.) as part of contouring efforts. Further, clinicalattributes obtained via the disclosure can help to unify disparatesources of data (such as molecular characteristics found on a geneticsequencing report, structured clinical data obtained from pathologyreports, imaging features and characteristics extracted from imaging).As a result, radiomic and imaging specific machine learning algorithmscan become more robust through the availability of this additional data,such as by using the data linked in step 508 as inputs to thosealgorithms at step 510. Furthermore, the imaging itself may or may notcome with diagnosis and/or phenotypic attributes included so the linkagebetween the imaging data and the related information that can beextracted from source documents via the invention can help resolve gapsin data.

5: Knowledge Database Curation and Additions

Turning to FIG. 24, yet another method 600 for implementing the presentsystem is depicted. At step 602, the mobile device may be used tocapture a document such as a NGS report, the document including medicalinformation such as sequencing information about a patient. At step 604,an entity linking engine may be used to extract at least some of thatinformation, such as using the techniques described above. At step 606,that information then may be provided to one or more data repositories,such as in a structured format. In addition to this patient-specificdata, the system also may process journal articles from medicalpublications by similarly extracting structured medical information fromthose sources at step 608 and then adding that structured information tothe data repository at step 610 to curate a knowledge database basedupon features of each report which are relevant to each databasespecialization. For example, a knowledge database for cancer treatmentsmay desire to receive new articles which are relevant by filtering newlypublished articles to find articles which are oncology and treatmentfocused which may be added into the knowledge database along with keywords, phrases, and other indexable features. The new entry may then bereviewed for curation or automatically entered into the knowledgedatabase.

6: Facility-Based Records Sync for Facilities that do not Easily ShareData

The disclosure above may also serve as a means to easily integrate EMRsystems which are not synced. For example, turning to FIG. 25, yetanother method 700 for implementing the present system is depicted. Atstep 702, the mobile device may be used to capture a document such as aNGS report, the document including medical information such assequencing information about a patient. At step 704, an entity linkingengine may be used to extract at least some of that information, such asusing the techniques described above. At step 706, that information thenmay be provided to one or more data repositories, such as in astructured format. A patient receiving treatment at an institution whichis geographically distance from their home may desire to report to alocal institution for testing and lab results. The local institution maynot sync their EMR with the primary institution and only provide adocument with the testing or lab reports to the primary institution. Theinstant disclosure may allow the primary institution to sync the reportwith their EMR by quickly scanning the report once received, as at step708.

7. Adding to De-Identified Data Sets

A physician may wish to take the information provided on a lab reportand ingest it into a data platform that is unconnected from the providerof the lab report. Thus, turning to FIG. 26, yet another method 800 forimplementing the present system is depicted. At step 802, the mobiledevice may be used to capture a document such as a NGS report, thedocument including medical information such as sequencing informationabout a patient. At step 804, an entity linking engine may be used toextract at least some of that information, such as using the techniquesdescribed above. At step 806, that information then may be provided toone or more data repositories, such as in a structured format. At step808, the data platform may allow the physician to view the patientinformation from the report in the context of a larger data set of“like” patients, whom may have received NGS from different clinicallaboratories.

8. Tumor Board

Turning to FIG. 27, yet another method 900 for implementing the presentsystem is depicted. At step 902, the mobile device may be used tocapture a document such as a NGS report, the document including medicalinformation such as sequencing information about a patient. At step 904,an entity linking engine may be used to extract at least some of thatinformation, such as using the techniques described above. At step 906,that information then may be provided to one or more data repositories,such as in a structured format. At that point, a physician may wish totake the information provided on a lab report and ingest it into a dataplatform that provides tumor board functionality to the physician, as atstep 908. An exemplary tumor board platform may provide functionality topermit physicians to review the cases of multiple patients, one at atime, and review patient characteristics (such as age, molecularprofile, clinical profile, gender, race, and so forth) to determine themost appropriate treatment for the patient. The tumor board platform maypermit multiple clinicians to sit in a single location, such as a room,and view the clinical information about each patient, as at step 910.Or, the platform may be virtual, allowing multiple clinicians to sit indisparate locations while simultaneously reviewing a patient'sinformation, as at step 912.

9. Alternative Clinical Decision Support

Different clinical laboratories use different bioinformatics platforms,and calling a variant on a gene does not necessarily mean that aclinical laboratory will suggest the same treatment as another clinicallab that calls the same variant. Thus, turning to FIG. 28, still anothermethod 1000 for implementing the present system is depicted. At step1002, the mobile device may be used to capture a document such as a NGSreport, the document including medical information such as sequencinginformation about a patient, as well as one or more of a type oftreatment, dosage of treatment, duration of treatment, immunologymarkers, potential clinical trial(s) available to the patient, etc.Exemplary immunology markers include, but are not limited to, PD-1expression, other checkpoint inhibitor indicators (such as CTLA-4),immune cell infiltration, immunohistochemistry (IHC) indicators, tumorinfiltrating lymphocyte indicators, monoclonal antibody indicators,vaccine/adjuvant indicators such as tumor cell vaccines, antigenvaccines, dendritic cell vaccines, vector-based vaccines, oncolyticviruses, CAR T-cell therapy, etc. At step 1004, an entity linking enginemay be used to extract at least some of that information, such as usingthe techniques described above. At step 1006, that information then maybe provided to one or more data repositories, such as in a structuredformat, the data repositories including the relevant types of treatment,dosages of treatment, durations of treatment, immunology markers,potential clinical trial(s) available to the patient, etc., for patientswith similar sequencing information, where the information presented inthe NGS report may be different from the relevant counterparts stored inthe data repositories. At step 1008, the system may display a subset ofthe extracted data, such as the patient's identified mutations andvariants. By permitting capture of clinical variants, a physician may beable to get a “second opinion” on the type of treatment, dosage oftreatment, duration of treatment, immunology markers, and so forth.Likewise, at step 1010, the system may display one or more clinicaltrials potentially available to the patient, as discussed above. In thismanner, by comparing and displaying the reported information againsttheir potentially available counterparts, the physician may get a“second opinion” on clinical trials that may be appropriate for thepatient.

As seen in FIG. 29, a system 1100 may include a server 1102 including orin communication with a first database 1102 and a second database 1104.In one aspect, the first database 1102 may include patient-specificinformation, such as elements of each patient's EHR or EMR data. Thesecond database 1104 may be a knowledge-database that includespatient-agnostic medical information, such as genetic variants and theirrelated mutation effects for observed and classified variants for eachgene, medications or other treatments relevant to the genetic variants,articles relevant to those variants, etc. The second database 1104further may include mask or template-based information to enable thesystem to more efficiently extract information from one or moretemplate-style documents. It will be appreciated that the first andsecond databases may be combined into a single database or,alternatively, that one or both of those databases individually mayactually be a plurality of different databases, such as to assist indata segregation or improved processing by optimizing database calls forthe requested different types of data.

Staying with FIG. 29 the server 1102 may be in communication with one ormore mobile devices, such as smartphones 1108A, 1108B, tablet devices1108C, 1108D, and laptop or other computing devices 1108E. In oneaspect, the server 1102 may be connected directly to one or more of thedevices, such as via an Ethernet or other suitable connection.Alternatively, the server 1102 may be connected wirelessly to one ormore of the devices, such as via WiFi or another wireless connection, aswould be appreciated by those of ordinary skill in the relevant art. Asdiscussed herein, one or more analytical actions described herein may beperformed by the mobile devices. Additionally or alternatively, one ormore actions may be performed by the server, such as the mobile devicesmay be used to create new patient records and capture electronic imagesof documents relating to patients, while the server may be employed toperform the OCR and/or other analytics described above on the captureddocuments.

While the foregoing written description of the invention enables one ofordinary skill to make and use what is considered presently to be thebest mode thereof, those of ordinary skill will understand andappreciate the existence of variations, combinations, and equivalents ofthe specific exemplary embodiment and method herein. The inventionshould therefore not be limited by the above described embodiment andmethod, but by all embodiments and methods within the scope and spiritof the invention as claimed.

1. A method performed by a clinical laboratory, comprising: a. receivingat least one specimen of, and medical history information about, acancer patient; b. performing next generation sequencing on the at leastone specimen to generate molecular information comprising at least fivemillion reads; c. arranging the medical history information of thepatient into structured medical history information; d. storing thestructured medical history information in a database system; e.uploading the molecular information to a cloud service for processing bya variant calling bioinformatics pipeline; f. generating one or morevariant calls resulting from processing of the molecular information bythe bioinformatics pipeline; g. determining a variant classificationreflective of a degree of pathogenicity of each of the one or morevariant calls; h. storing in the database system the one or more variantcalls and each variant call's corresponding pathogenic interpretation;i. preparing a treatment plan comprising one or more of a therapyidentification or a therapy efficacy, based on the structured medicalhistory information, the one or more variant calls, and thecorresponding pathogenic interpretation stored in the database system;and j. preparing a report including the one or more variant calls, thecorresponding pathogenic interpretation, and the treatment plan.
 2. Themethod of claim 1, where the therapy identification is a therapy name.3. The method of claim 1, where the therapy identification is a therapyclass.
 4. The method of claim 1, where the therapy identification is aclinical trial.
 5. The method of claim 3, where the therapy class is aradiation therapy.
 6. The method of claim 3, where the therapy class isa chemotherapy.
 7. The method of claim 3, where the therapy class is animmunotherapy.
 8. The method of claim 3, where the therapy class is aPARP inhibitor.
 9. The method of claim 1, where the therapyidentification is a course of therapy.
 10. The method of claim 1, wherethe therapy efficacy is an indication of therapy resistance.
 11. Themethod of claim 1, where the therapy efficacy is an indication oftherapy response.
 12. The method of claim 1, where the treatment plan isprepared at least in part using a therapy matching engine.
 13. Themethod of claim 1, where the treatment plan ranks therapies based on theone or more variant calls.
 14. The method of claim 1, where thetreatment plan ranks therapies based on the pathogenic interpretationcorresponding to the one or more variant calls.
 15. The method of claim1, where the treatment plan ranks therapy identification based onwhether the patient's cancer type matches a cancer type associated withan evidence level associated with the therapy identification.
 16. Themethod of claim 1, where the treatment plan is prepared using a therapymatching engine.
 17. The method of claim 16, where the therapy matchingengine automatically determines that the one or more variant calls areassociated with an evidence level associated with the therapyidentification.
 18. The method of claim 1, where the report is preparedas a Portable Document Format document.
 19. The method of claim 1,further comprising displaying the report on a mobile device.
 20. Themethod of claim 1, where the at least one specimen comprises a FFPEslide and a normal specimen.
 21. The method of claim 1, where the atleast one specimen comprises a normal sample and a tumor sample, wherethe processing of the molecular information by the bioinformaticspipeline comprises subtracting variants detected in the normal samplefrom variants detected in the tumor sample.
 22. The method of claim 1,where the molecular information generated by next generation sequencingcomprises ribonucleic acid sequences.
 23. The method of claim 1, wherethe molecular information generated by next generation sequencingcomprises ribonucleic acid sequences indicating fusion mRNAs.
 24. Themethod of claim 1, further comprising determining whether the generatedmolecular information meets a quality threshold level of a number ofread pairs of ribonucleic acid sequences.
 25. The method of claim 1,where the variant calls resulting from the processing of the molecularinformation by the bioinformatics pipeline comprise single nucleotidepolymorphisms, indels, copy number variants, and gene rearrangements.26. The method of claim 1, where the step of arranging the medicalhistory information of the patient into structured medical historyinformation comprises using an optical character recognitionmicroservice to consume clinical records.
 27. The method of claim 1,further comprising preparing the treatment plan based on results ofapplying a cancer treatment to an organoid developed from a tumorspecimen of the patient.
 28. The method of claim 1, further comprisingpreparing the treatment plan based on one or more features extractedfrom a radiology image associated with the patient.
 29. The method ofclaim 1, further comprising preparing the treatment plan based on one ormore features extracted from a slide image associated with the patient.30. The method of claim 1, further comprising: k. storing informationfrom the treatment plan and the report in structured form in asearchable database comprising at least ten thousand records, eachrecord comprising information stored in structured form from anothertreatment plan and another report associated with a patient with cancer;and l. providing an interface for a recipient of the report to query thesearchable database.